On the Use of a Supramolecular Coarse‐Grained Model for the Solvent in Simulations of the Folding Equilibrium of an Octa‐β‐peptide in MeOH and H2O

Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse‐grained (CG) solvent MeOH and H₂O models to speed up the sampling of the conformational equilibria of an octa‐β‐peptide is investigated. This peptide is thought to predominantly adopt a 3₁₄‐helical fold when solvated in MeOH, and a hairpin fold when solvated in H₂O on the basis of the NMR data. Various factors such as the chirality of a residue, a force‐field modification for the solute, coarse‐graining of the solvent model, and an extension of the nonbonded interaction cut‐off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa‐β‐peptide.     

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.     

NMR‐Solution Structures in Methanol of an α‐Heptapeptide,of a β3/β2‐Nonapeptide,and of an all‐β3‐Icosapeptide Carrying the 20 Proteinogenic Side Chains

The NMR‐solution structure of an α‐heptapeptide with a central Aib residue was investigated in order to verify that, in contrast to β‐peptides, short α‐peptides do not form a helical structures in MeOH. Although the central Aib residue was found to induce a bend in the experimentally determined structure, no secondary structure typical for longer α‐peptides or proteins was found. A β²/β³‐nonapeptide with polar, positively charged side chains was subjected to NMR analysis in MeOH and H₂O. Whereas, in MeOH, it folds into a 10/12‐helix very similar to the structure determined for a corresponding β²/β³‐nonapeptide with only aliphatic side chains, no dominant conformation could be determined in H₂O. Finally, the NMR analysis of a β³‐icosapeptide containing the side chains of all 20 proteinogenic amino acids in MeOH is described. It revealed that this 20mer folds into a 3₁₄‐helix over its whole length forming six full turns, the longest 3₁₄‐helix found so far. Together, our findings confirm that, in contrast to α‐peptides, β‐peptides not only form helices with just six residues, but also form helices that are longer than helical sections usually observed in proteins or natural peptides. The higher helix‐forming propensity of long β‐peptides is attributed to the conformation‐stabilizing effect of the staggered ethane sections in β‐peptides which outweighs the detrimental effect of the increasing macrodipole.     

The anti‐inflammatory triterpenoid methyl 2‐cyano‐3,12‐dioxooleana‐1,9(11)‐dien‐28‐oate methanol solvate hydrate

The title compound, C₃₂H₄₃NO₄·CH₄O·H₂O, has a nearly planar cyano‐enone A ring in an otherwise normal oleanane triterpenoid. Rings A, B and C are non‐chairs, but rings D and E adopt essentially cyclo­hexane chair conformations. The structure clearly establishes the C‐D‐E ring stereochemistry as trans‐syn‐cis, as predicted from a nuclear Overhauser effect (NOE) NMR measurement.     

NMR‐Structural Investigations of a β3‐Dodecapeptide with Proteinogenic Side Chains in Methanol and in Aqueous Solutions

The structural properties of an all‐β³‐dodecapeptide with the sequence H‐β‐HLys(N^ε‐CO(CH₂)₃‐S Acm)‐β‐HPhe‐β‐HTyr‐β‐HLeu‐β‐HLys‐β‐HSer‐β‐HLys‐β‐HPhe‐β‐HSer‐β‐HVal‐β‐HLys‐β‐HAla‐OH ( 1 ) have been studied by two‐dimensional homonuclear ¹H‐NMR and by CD spectroscopy. In MeOH solution, high‐resolution NMR spectroscopy showed that the β‐dodecapeptide forms an (M)‐3₁₄‐helix, and the CD spectrum corresponds to the pattern expected for an (M)‐3₁₄‐helical secondary structure. In aqueous solution, however, the peptide adopts a predominantly extended conformation without regular secondary‐structure elements, which is in agreement with the absence of the characteristic trough near 215 nm in the CD spectrum. The NMR and CD measurements with solutions of 1 in MeOH containing 3M urea further indicated that the peptide retains the regular secondary structural elements under these conditions, whereas, after addition of 40% (v/v) H₂O to the MeOH solution, the large ¹H‐chemical‐shift dispersion indicative of a defined spatial peptide fold was lost. The β³‐dodecapeptide is – so far – the longest β‐peptide shown to adopt a regular (M)‐3₁₄‐helix conformation in an organic solvent. The observation that the structure of this long β³‐peptide is not maintained in aqueous solution indicates that the (M)‐3₁₄‐fold is primarily stabilized by short‐range interactions.     

Molecular and Supramolecular Structures of 1‐Phenyl‐4‐phenylacetyl‐2‐thiosemicarbazide (H2L) and its Complexes with Diphenyllead(IV) Chloride and Acetate

Reaction of 1‐phenyl‐4‐phenylacetyl‐2‐thiosemicarbazide (H₂L) with diphenyllead(IV) dichloride and acetate afforded the complexes [PbPh₂Cl₂(H₂L)₂] and [PbPh₂L]. The ligand and the complexes were characterized by elemental analyses, ¹H and ¹³C NMR spectroscopy and X‐ray crystallography. In the asymmetric unit of crystals of the ligand there are four independent molecules of H₂L and four molecules of water, which associate in the lattice as two independent sheets. The complex [PbPh₂Cl₂(H₂L)₂]·4MeOH has slightly distorted all‐trans octahedral geometry around the lead atom, and the fact that the ligand is S‐bound rather than O‐bound suggests that PbPh₂Cl₂ behaves as a “soft” Lewis acid. Hydrogen bonds involving NH groups, Cl atoms and MeOH molecules form a three‐dimensional supramolecular structure. In [PbPh₂L]·Me₂CO, the L^2? anion bridges between two metal centres, binding to one strongly via the N and S atoms and weakly via the O atom, and to the other via the O atom, thus creating polymeric chains along the b axis. The double deprotonation and metallation of H₂L induce significant changes in its configuration and lengthen the C‐S and C‐O bonds, suggesting an evolution of the dianion towards a thiol‐enol form.     

Influence of 1,4‐dioxane solvent inclusion on the crystal structure of 5,5′‐diphenyl‐2,2′‐(p‐phenylene)di‐1,3‐oxazole (POPOP)

Crystallization of 5,5′‐diphenyl‐2,2′‐(p‐phenylene)di‐1,3‐oxazole (POPOP), C₂₄H₁₆N₂O₂, from chloroform or 1,4‐dioxane yielded crystals in pure and solvated forms, respectively. The solvated crystals of POPOP were found to contain 1,4‐dioxane in a strict 1:2 compound–solvent stoichiometry, C₂₄H₁₆N₂O₂·C₄H₈O₂, thus being a defined solvent‐inclusion compound. The crystal system is monoclinic in both cases and the asymmetric unit of the cell contains only half of the molecule (plus one dioxane molecule in the case of the solvated structure), owing to the centrosymmetry of the di‐1,3‐oxazole molecule.     

Solid‐Phase Synthesis of a β‐Dodecapeptide with Seven Functionalized Side Chains and CD‐Spectroscopic Evidence for a Dramatic Structural Switch When Going from Water to Methanol Solution

An all‐β³‐dodecapeptide with a protected N‐terminal thiol‐anchoring group and with seven side chains has been synthesized in multi‐mg amounts by the manual solid‐phase technique, applying Fmoc methodology and the Wang resin. The sequence is β‐HLys‐β‐HPhe‐β‐HTyr‐β‐HLeu‐β‐HLys‐β‐HSer‐β‐HLys‐β‐HPhe‐β‐HSer‐β‐HVal‐β‐HLys‐β‐HAla‐OH (from N‐ to C‐terminus; see 1 ). The functional groups in the side chains of the building blocks were Boc (β‐HLys) or t‐Bu ether (β‐HSer, β‐HTyr) protected to allow for simultaneous deprotection and detachment from the resin with trifluoroacetic acid. All coupling steps were achieved with HBTU (=O‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyl uronium hexafluorophosphate)/HOBt (=1‐hydroxy‐1H‐benzotriazole) in DMF. For Fmoc (=(9H‐fluoren‐9‐yl)methoxycarbonyl) deprotection, a protocol was developed to surmount the previously reported problems arising in solid‐phase synthesis of β‐peptides when the chain length exceeds seven or eight amino‐acid moieties: for up to seven amino acids, a 20% solution of piperidine in DMF was used for removal of Fmoc; for the subsequent five amino acids, DBU and piperidine were employed for complete deprotection. The crude product was purified by preparative reversed‐phase HPLC, and the yield of pure β‐dodecapeptide derivative ( 1 ) was 23%. As the compound is well‐soluble in H₂O, it was characterized by ¹H‐NMR (in MeOH and H₂O), ¹³C‐NMR (in MeOH), and CD spectroscopy (in MeOH and in H₂O at pH values ranging from 3.5 to 11), and its molecular weight and composition were confirmed by high‐resolution mass spectrometry (Figs. 1 – 4). In MeOH solution, the β‐dodecapeptide exhibits the expected CD pattern typical of an (M)‐3₁₄‐helical secondary structure. In H₂O, however, the characteristic trough near 215 nm is missing in the CD spectrum, only a strong positive Cotton effect at 202 nm was observed, indicating the presence of β‐peptidic secondary structures, containing ten‐membered H‐bonded rings, such as the 12/10 helix (Fig. 4, right) or the hairpin. Only a detailed NMR solution‐structure analysis will provide the clues necessary for understanding the effects leading to the observed dramatic structural change of the highly functionalized β‐dodecapeptide described.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

Designed Beta‐Turn Mimic Based on the Allylic‐Strain Concept: Evaluation of Structural and Biological Features by Incorporation into a Cyclic RGD Peptide (Cyclo(‐L‐arginylglycyl‐L‐α‐aspartyl‐))

The (3R,5S,6E,8S,10R)‐11‐amino‐3,5,8,10‐tetramethylundec‐6‐enoic acid (ATUA; 1 ), which was designed as a βII′‐turn mimic according to the concepts of allylic strain and 2,4‐dimethylpentane units, was incorporated into a cyclic RGD peptide. The three‐dimensional structure of cyclo(‐RGD‐ATUA‐) (=cyclo(‐Arg‐Gly‐Asp‐ATUA‐)) 4 in H₂O was determined by NMR techniques, distance geometry calculations and molecular‐dynamics simulations. The RGD sequence of 4 shows high conformational flexibility but some preference for an extended conformation. The structural features of the RGD sequence of 4 were compared with the RGD moiety of cyclo(‐RGDfV‐) (=cyclo(‐Arg‐Gly‐Asp‐D ‐Phe‐Val‐)). In contrast to cyclo(‐RGDfV‐), which is a highly active αvβ3 antagonist and selective against αIIbβ3, cyclo(‐RGD‐ATUA‐) shows a lower activity and selectivity. The structure of the ATUA residue in the cyclic peptide resembles a βII′‐turn‐like conformation. Its middle part, adjacent to the C?C bond, strongly prefers the designed and desired structure.     

tert‐Butyl (3S,6R,9R)‐(5‐oxo‐3‐{[1(R)‐phenyl­ethyl]­carbamoyl}‐1,2,3,5,6,7,8,8a‐octa­hydro­indolizin‐6‐yl)­carbamate monohydrate at 95 K

The asymmetric unit of the title compound, C₂₂H₃₁N₃O₄·H₂O, incorporates one water mol­ecule, which is hydrogen bonded to the 3‐oxo O atom of the indolizidinone system. The two rings of the peptidomimetic mol­ecule are trans‐fused, with the six‐membered ring having a slightly distorted half‐chair conformation and the five‐membered ring having a perfect envelope conformation. The structure is stabilized by intermolecular O—H?O interactions between the water and adjacent peptide mol­ecules, and by N—H?O interactions between the peptide mol­ecules, which link the mol­ecules into infinite chains.     

7‐Hydroxy‐5‐methoxy‐6,8‐dimethylflavanone: a natural flavonoid

The title flavonoid [systematic name: (2S)‐7‐hydroxy‐5‐methoxy‐6,8‐dimethyl‐2‐phenyl‐3,4‐dihydrochromen‐4(2H)‐one], C₁₈H₁₈O₄, displays statistical conformational disorder, with three conformations of the molecule involving three orientations of the phenyl ring and two orientations of the fused heterocyclic ring. The conformational disorder is correlated with the isomerization equilibrium between the flavanone and chalcone forms. The conformational behaviour has a potential impact on the biological activity of this class of compounds. Moreover, π stacking interactions at van der Waals distances are present between the aromatic rings of chroman‐4‐one groups of symmetry‐related molecules. Apart from these π–π interactions, molecules are linked by strong O—H...O hydrogen bonds between hydroxy and carbonyl groups.     

Different interaction motifs of dipolar S=O...C=O contacts that associate diastereomers of 2,4(6)‐di‐O‐benzoyl‐6(4)‐O‐{[(1S)‐7,7‐dimethyl‐2‐oxobicyclo[2.2.1]heptan‐1‐ylmethyl]sulfonyl}‐myo‐inositol 1,3,5‐orthoacetate

Diastereomeric mixtures of 2,4(6)‐di‐O‐benzoyl‐6(4)‐O‐[(1S)‐10‐camphorsulfonyl]‐myo‐inositol 1,3,5‐orthoesters associate in their crystal structures via different geometries of S=O...C=O short contacts, depending upon the substitution. A comparison of the dimeric association in the orthoacetate and orthoformate (solvated) derivatives shows a sheared parallel motif of dipolar S=O...C=O contacts bridging the former, whereas perpendicular S=O...C=O contacts occur in the latter. The title compound, C₃₂H₃₄O₁₁S, is chiral, owing to the presence of the camphor moiety.     

N‐(l‐2‐Aminobutyryl)‐l‐alanine and 2‐(l‐alanylamino)‐l‐butyric acid 0.33‐hydrate

The crystal structure of N‐(l ‐2‐amino­butyryl)‐l ‐alanine, C₇H₁₄N₂O₃, is closely related to the structure of l ‐alanyl‐l ‐alanine, both being tetragonal, while the retro‐analogue 2‐(l ‐alanyl­amino)‐l ‐butyric acid 0.33‐hydrate, C₇H₁₄N₂O₃·­0.33H₂O, forms a new type of molecular columnar structure with three peptide mol­ecules in the asymmetric unit.     

[2+2] Photocycloaddition of 2‐Morpholinoprop‐2‐enenitrile to Perinaphthenone

Perinaphthenone (=1H‐phenalen‐1‐one), known for efficient population of its T₁ (π,π*) state and suggested as a standard sensitizer for singlet oxygen (¹Δg) formation, forms a single stereoisomer of a head‐to‐tail [2+2] photoadduct across its C(2)=C(3) bond with 2‐morpholinoprop‐2‐enenitrile in benzene by broad band UV excitation (λ≥280 nm). The reaction is advantageously run to low conversion of starting materials only. The structure of the adduct, especially the relative configuration at C(9), has been derived from ¹H‐NMR data including NOE signal enhancement studies.     

2‐[(E)‐(4‐Hydroxy‐3‐methoxybenzylidene)amino]‐N‐(2‐methylphenyl)‐4,5,6,7‐tetrahydro‐1‐benzothiophene‐3‐carboxamide

The title compound, C₂₄H₂₄N₂O₃S, exhibits antifungal and antibacterial properties. The compound crystallizes with two molecules in the asymmetric unit, with one molecule exhibiting `orientational disorder' in the crystal structure with respect to the cyclohexene ring. The o‐toluidine groups in both molecules are noncoplanar with the respective cyclohexene‐fused thiophene ring. In both molecules, there is an intramolecular N—H...N hydrogen bond forming a pseudo‐six‐membered ring which locks the molecular conformation and eliminates conformational flexibility. The crystal structure is stabilized by O—H...O hydrogen bonds; both molecules in the asymmetric unit form independent chains, each such chain consisting of alternating `ordered' and `disordered' molecules in the crystal lattice.     

3β‐(Stearyloxy)olean‐12‐ene from Austroplenckia populnea: Structure Elucidation by 2D‐NMR and Quantitative 13C‐NMR Spectroscopy

3β‐(Stearyloxy)olean‐12‐ene was isolated from a hexane extract of Austroplenckia populnea Reiss (Celastraceae) leaves. The structure was solved by means of quantitative ¹³C‐NMR, HMBC, HMQC, COSY, NOESY, and NOE difference spectra. The mass spectrum showed an [M+1]⁺ ion peak at m/z 693, and the molecular formula C₄₈H₈₄O₂ was confirmed by combustion analysis.     

NMR and conformational studies of new 5‐phenylpyrrole‐carboxamide derivatives

The ¹H and ¹³C NMR resonances of 22 5‐(5‐substituted‐2‐nitrophenyl)‐1H‐pyrrole‐2‐carboxamides, 22 5‐(5‐substituted‐2‐aminophenyl)‐1H‐pyrrole‐2‐carboxamides, and 9 5‐phenyl‐1H‐pyrrole‐2‐carboxamides were assigned completely using the concerted application of one‐ and two‐dimensional experiments (DEPT, gs‐HMQC and gs‐HMBC). NOE studies and conformational analysis confirm the preferred conformations of such compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Gas‐phase fragmentation reactions of protonated benzofuran‐ and dihydrobenzofuran‐type neolignans investigated by accurate‐mass electrospray ionization tandem mass spectrometry

We have investigated gas‐phase fragmentation reactions of protonated benzofuran neolignans (BNs) and dihydrobenzofuran neolignans (DBNs) by accurate‐mass electrospray ionization tandem and multiple‐stage (MSⁿ) mass spectrometry combined with thermochemical data estimated by Computational Chemistry. Most of the protonated compounds fragment into product ions B ([M + H–MeOH]⁺), C ([ B –MeOH]⁺), D ([ C –CO]⁺), and E ([ D –CO]⁺) upon collision‐induced dissociation (CID). However, we identified a series of diagnostic ions and associated them with specific structural features. In the case of compounds displaying an acetoxy group at C‐4, product ion C produces diagnostic ions K ([ C –C₂H₂O]⁺), L ([ K –CO]⁺), and P ([ L –CO]⁺). Formation of product ions H ([ D –H₂O]⁺) and M ([ H –CO]⁺) is associated with the hydroxyl group at C‐3 and C‐3′, whereas product ions N ([ D –MeOH]⁺) and O ([ N –MeOH]⁺) indicate a methoxyl group at the same positions. Finally, product ions F ([ A –C₂H₂O]⁺), Q ([ A –C₃H₆O₂]⁺), I ([ A –C₆H₆O]⁺), and J ([ I –MeOH]⁺) for DBNs and product ion G ([ B –C₂H₂O]⁺) for BNs diagnose a saturated bond between C‐7′ and C‐8′. We used these structure‐fragmentation relationships in combination with deuterium exchange experiments, MSⁿ data, and Computational Chemistry to elucidate the gas‐phase fragmentation pathways of these compounds. These results could help to elucidate DBN and BN metabolites in in vivo and in vitro studies on the basis of electrospray ionization ESI‐CID‐MS/MS data only.     

(3,8,9,14‐Tetraethyl‐2,4,13,15‐tetramethyltripyrrinato)(trifluoroacetato)­palladium(II)

In the crystal structure, the title compound {systematic name: [2,5‐bis­(4‐ethyl‐3,5‐dimethyl‐2H‐pyrrol‐2‐ylidene­meth­yl)‐1H‐pyrrolato](trifluoroacetato)palladium(II)}, [Pd(C₂F₃O₂)(C₂₇H₃₄N₃)], forms chiral mol­ecules with a helical distortion of the tripyrrinate ligand backbone and an essentially planar PdN₃O core, with Pd—N distances ranging from 1.977 (3) to 2.045 (3) Å and a Pd—O distance of 2.051 (2) Å. This distortion of the organic ligand is considered as the conformational answer to the steric inter­action of the terminal methyl groups of the tripyrrinate ligand with the donor O atom of the trifluoro­acetate group.