Experimental and Computational Models for Side Chain Discrimination in Peptide-Protein Interactions.

A bis(18-crown-6) Tröger's base receptor and 4-substituted hepta-1,7-diyl bisammonium salt ligands have been used as a model system to study the interactions between non-polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all-anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor-ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl- and a phenyl group to an aromatic cavity, via CH-π, and combined aromatic CH-π and π-π interactions to be -1.7 and -3.3 kJ mol-1 , respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.

ß-Mannanase-catalyzed synthesis of alkyl mannooligosides.

ß-Mannanases catalyze the conversion and modification of ß-mannans and may, in addition to hydrolysis, also be capable of transglycosylation which can result in enzymatic synthesis of novel glycoconjugates. Using alcohols as glycosyl acceptors (alcoholysis), ß-mannanases can potentially be used to synthesize alkyl glycosides, biodegradable surfactants, from renewable ß-mannans. In this paper, we investigate the synthesis of alkyl mannooligosides using glycoside hydrolase family 5 ß-mannanases from the fungi Trichoderma reesei (TrMan5A and TrMan5A-R171K) and Aspergillus nidulans (AnMan5C). To evaluate ß-mannanase alcoholysis capacity, a novel mass spectrometry-based method was developed that allows for relative comparison of the formation of alcoholysis products using different enzymes or reaction conditions. Differences in alcoholysis capacity and potential secondary hydrolysis of alkyl mannooligosides were observed when comparing alcoholysis catalyzed by the three ß-mannanases using methanol or 1-hexanol as acceptor. Among the three ß-mannanases studied, TrMan5A was the most efficient in producing hexyl mannooligosides with 1-hexanol as acceptor. Hexyl mannooligosides were synthesized using TrMan5A and purified using high-performance liquid chromatography. The data suggests a high selectivity of TrMan5A for 1-hexanol as acceptor over water. The synthesized hexyl mannooligosides were structurally characterized using nuclear magnetic resonance, with results in agreement with their predicted ß-conformation. The surfactant properties of the synthesized hexyl mannooligosides were evaluated using tensiometry, showing that they have similar micelle-forming properties as commercially available hexyl glucosides. The present paper demonstrates the possibility of using ß-mannanases for alkyl glycoside synthesis and increases the potential utilization of renewable ß-mannans.

A Remarkably Complex Supramolecular Hydrogen-Bonded Decameric Capsule Formed from an Enantiopure C2-Symmetric Monomer by Solvent-Responsive Aggregation.

The formation of an unprecedented decameric capsule in carbon disulfide, held together by the combination of double and triple hydrogen bonds between isocytosine units embedded in an enantiomerically pure bicyclic framework is reported. The aggregation occurs via symmetry breaking of the enantiopure intrinsically C2-symmetric monomer brought about by solvent, induced tautomerization of the hydrogen-bonding unit. We show that the topology of the aggregate is responsive to the solvent in which the assembly takes place. In this study we demonstrate that in carbon disulfide the chiral decameric cavity aggregate consisting of three forms of the same monomer, differing in their hydrogen bonding to each other is selectively formed, representing a tube-like structure capped with two C2-symmetric monomers. The large cylindrical cavity produced selectively accommodates one partially solvated C60 molecule, and molecular dynamic simulations revealed the special role of the solvent in the inclusion mechanism. The strategy described herein represents the first step toward the creation of a new class of hydrogen-bonded tubular objects from only one small symmetric building block by solvent-responsive aggregation.

A heteroleptic ferrous complex with mesoionic bis(1,2,3-triazol-5-ylidene) ligands: taming the MLCT excited state of iron(II).

Strongly σ-donating N-heterocyclic carbenes (NHCs) have revived research interest in the catalytic chemistry of iron, and are now also starting to bring the photochemistry and photophysics of this abundant element into a new era. In this work, a heteroleptic Fe(II) complex (1) was synthesized based on sequentially furnishing the Fe(II) center with the benchmark 2,2'-bipyridine (bpy) ligand and the more strongly σ-donating mesoionic ligand, 4,4'-bis(1,2,3-triazol-5-ylidene) (btz). Complex 1 was comprehensively characterized by electrochemistry, static and ultrafast spectroscopy, and quantum chemical calculations and compared to [Fe(bpy)3](PF6)2 and (TBA)2[Fe(bpy)(CN)4]. Heteroleptic complex 1 extends the absorption spectrum towards longer wavelengths compared to a previously synthesized homoleptic Fe(II) NHC complex. The combination of the mesoionic nature of btz and the heteroleptic structure effectively destabilizes the metal-centered (MC) states relative to the triplet metal-to-ligand charge transfer ((3)MLCT) state in 1, rendering it a lifetime of 13 ps, the longest to date of a photochemically stable Fe(II) complex. Deactivation of the (3)MLCT state is proposed to proceed via the (3)MC state that strongly couples with the singlet ground state.

Differentiation and quantification of synthetic phosphatidylethanol (PEth) homologues by ¹H- and ¹³C-NMR in polar organic solvents.

Various phosphatidylethanol (PEth) derivatives, the corresponding reversed positional isomers (RPI-PEths), lyso-PEth-16:0, and penta-deuterium-labeled PEth analogs (d5-PEths), were synthesized by enzyme-independent synthetic routes. A general solvent system consisting of a mixture of acetone-d6 and methanol-d4 (97:3; v/v) was found to provide a good solubilizing capacity and excellent hydrogen-1 NMR ((1)H-NMR) peak resolution of various PEth homologues. Analytical differentiation of PEth from the corresponding RPI-PEth by carbon-13 NMR ((13)C-NMR) was demonstrated by comparison of the (13)C-NMR signals of the carbonyl groups, the allylic positions, and of the ß-carbons. An exemplary stable long-term room temperature, DMSO-d6-based, and proton-sensitive quantitative nuclear magnetic resonance ((1)H-qNMR) independently quantified calibrator comprising PEth-16:0/18:1 for liquid chromatography (tandem) mass spectrometry (LC-MS/MS) analytical applications were prepared by employment of sodium dodecyl sulfate (SDS) as a solubilizing additive. In summary, novel hypothetically occurring PEth derivatives, e.g., RPI-PEths, have been independently synthesized with regio- and stereochemical control. Use of polar organic solvents, e.g., mixtures of acetone-d6 and methanol-d4 or DMSO-d6, improves spectral line shapes as compared to traditional hydrophobic solvents and allow for analytical differentiation between closely related PEth derivatives, as well as LC-MS/MS-independent concentration determination of dissolved single species by employment of (1)H-qNMR.

Composition- and size-controlled cyclic self-assembly by solvent- and C60-responsive self-sorting.

Synthesis, solvent-, and guest-controlled self-assembly, and self-sorting of new hydrogen-bonded chiral cavity receptors are reported. The design of the cavity is based on the cyclic self-aggregation of monomers containing the 4H-bonding ureidopyrimidinone motif fused with the bicylo[3.3.1]nonane framework. Selective formation of kinetically inert cyclic tetramers is observed in chloroform, while in toluene an equilibrium between tetrameric and pentameric forms exists. The high affinity of the tetrameric aggregates toward C60 and C70 is observed in aromatic solvents. The host-guest interaction of unconventional π-acidic supramolecular receptors for fullerenes is turned off and on by changing the solvent, whereas the selection of size and the very composition of the cavity aggregate is controlled by either the change of solvent or the addition of fullerene guest, making our systems a new type of self-sorting device.

Potential determining salts in microemulsions: interfacial distribution and effect on the phase behavior.

In this work we consider potential determining salts, also referred to as phase transfer agents for a future objective of electrochemistry at the oil-water interface in microemulsions. We have studied these salts, composed of a hydrophilic and a hydrophobic ion, in microemulsion stabilized by nonionic surfactants with an oligo ethylene oxide headgroup. NMR measurements show that the salts preferentially dissociate across the surfactant interface between the oil and water domains, and hence create a potential drop across the surfactant film, and back to back diffuse double layers in the oil and water phases. These observations are also supported by Poisson-Boltzmann calculations. This adsorption like event stabilizes the microemulsion. Repulsive long-range interactions between thin lamellae of surfactant and water lamellae in oil were observed using SAXS, thus confirming the presence of electrostatic forces mediated through the oil domain. We also observed that reversing the charges on the potential determining salts had opposite effects on the phase inversion temperature.

Synthesis and self-aggregation of enantiopure and racemic molecular tweezers based on the bicyclo[3.3.1]nonane framework.

A pair of molecular tweezers (syn-4) that consists of quinoline and pyrazine units fused to a bicyclic framework is presented. The tweezers were synthesised both as a racemic mixture (rac-4) and an enantiomerically pure form ((R,R,R,R)-4) starting from either racemic or enantiomerically pure bicyclo[3.3.1]nonane-2,6-dione (3). Homochiral dimers were observed in the solid state for rac-4. The self-association of both rac-4 and (R,R,R,R)-4 was studied in solution. A weak self-association constant in CDCl(3) was estimated by (1)H NMR spectroscopic dilution titration experiments in both cases, following several proton resonances. For this purpose, a general normalisation model for the accurate determination of association constants from multiple datasets was developed. In contrast to the solid state, no diastereomeric discrimination was observed for rac-4 in solution.

Luminescence and reactivity of a charge-transfer excited iron complex with nanosecond lifetime.

Iron's abundance and rich coordination chemistry are potentially appealing features for photochemical applications. However, the photoexcitable charge-transfer states of most iron complexes are limited by picosecond or subpicosecond deactivation through low-lying metal-centered states, resulting in inefficient electron-transfer reactivity and complete lack of photoluminescence. In this study, we show that octahedral coordination of iron(III) by two mono-anionic facial tris-carbene ligands can markedly suppress such deactivation. The resulting complex [Fe(phtmeimb)2]+, where phtmeimb is {phenyl[tris(3-methylimidazol-1-ylidene)]borate}-, exhibits strong, visible, room temperature photoluminescence with a 2.0-nanosecond lifetime and 2% quantum yield via spin-allowed transition from a doublet ligand-to-metal charge-transfer (2LMCT) state to the doublet ground state. Reductive and oxidative electron-transfer reactions were observed for the 2LMCT state of [Fe(phtmeimb)2]+ in bimolecular quenching studies with methylviologen and diphenylamine.

Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer.

The design and synthesis of new stimuli-responsive hydrogen-bonding monomers that display a diversity of self-assembly pathways is of central importance in supramolecular chemistry. Here we describe the aggregation properties of a simple, intrinsically C2-symmetric enantiopure bicyclic cavity compound bearing a terminally unsubstituted ureidopyrimidinone fragment fused with a pyrrole moiety in different solvents and in the absence and presence of C60 and C70 guests. The tetrameric cyclic aggregate is selectively obtained in chlorinated solvents, where only part of the available hydrogen bonding sites are utilized, whereas in toluene or upon addition of C70 guests, further aggregation into tubular supramolecular polymers is achieved. The open-end cyclic assemblies rearrange into a closed-shell capsule upon introduction of C60 with an accompanied symmetry breaking of the monomer. Our study demonstrates that a C60 switch can be used to simultaneously control the topology and occupancy of tubular assemblies resulting from the aggregation of small monomers.

A desymmetrization route to fused Troger's base analogues: synthesis, isolation, and characterization of the first anti-anti diastereomer of a fused tris-Troger's base analogue.

A desymmetrization route to fused Troger's base analogues was developed. In this way, the synthesis of the first example of an anti-anti diastereomer of a fused tris-Troger's base analogue was accomplished. The resulting compound 5b is a nonlinear symmetric regioisomer obtained from p-bromoaniline in 7% yield. The corresponding syn-anti diastereomer 5a was obtained in 4% yield.

Tröger's base twisted amides: endo functionalization and synthesis of an inverted crown ether.

Taking advantage of the unconventional reactivity of twisted mono- and bis-amides of Tröger's base (TB), rac-6 and rac-7, respectively, the first synthesis of a 6-endo-monosubstituted TB analogue, rac-9, and the first rational synthesis of a 6,12-endo,endo-disubstituted TB analogue, rac-11, have been achieved. The bis-TB crown ether, meso-13, was prepared starting from rac-7. Meso-13 constitutes a rare example of a crown ether with an inverted methylene bridge-to-bridge bis-TB conformation both in solution and in the solid state, resulting in a reluctance to act as a receptor for cations.

Microspectroscopic evidence of cretaceous bone proteins.

Low concentrations of the structural protein collagen have recently been reported in dinosaur fossils based primarily on mass spectrometric analyses of whole bone extracts. However, direct spectroscopic characterization of isolated fibrous bone tissues, a crucial test of hypotheses of biomolecular preservation over deep time, has not been performed. Here, we demonstrate that endogenous proteinaceous molecules are retained in a humerus from a Late Cretaceous mosasaur (an extinct giant marine lizard). In situ immunofluorescence of demineralized bone extracts shows reactivity to antibodies raised against type I collagen, and amino acid analyses of soluble proteins extracted from the bone exhibit a composition indicative of structural proteins or their breakdown products. These data are corroborated by synchrotron radiation-based infrared microspectroscopic studies demonstrating that amino acid containing matter is located in bone matrix fibrils that express imprints of the characteristic 67 nm D-periodicity typical of collagen. Moreover, the fibrils differ significantly in spectral signature from those of potential modern bacterial contaminants, such as biofilms and collagen-like proteins. Thus, the preservation of primary soft tissues and biomolecules is not limited to large-sized bones buried in fluvial sandstone environments, but also occurs in relatively small-sized skeletal elements deposited in marine sediments.

Expanding the scope of Lewis acid catalysis in water: remarkable ligand acceleration of aqueous ytterbium triflate catalyzed Michael addition reactions.

[reaction: see text] Significant rate acceleration of metal-catalyzed Michael addition reactions in water was observed upon addition of small, dibasic ligands. Ytterbium triflate and TMEDA was the most effective combination leading to a nearly 20-fold faster reaction than in the absence of ligand.

The synthesis and characterization of all diastereomers of a linear symmetrically fused Tris-Tröger's base analogue: new chiral cleft compounds.

The synthesis and characterization of all diastereomers of a linear symmetrically fused tris-Tröger's base analogue are described. The diastereomers are unambiguously assigned as syn-anti 1 a, anti-anti 1 b, and syn-syn 1 c isomers, by using X-ray diffraction analysis and NMR spectroscopy. For the first time, the anti-anti and the syn-syn diastereomers of a linear symmetrically fused tris-Tröger's base analogue have been synthesized. Molecules 1 a and 1 c are new cleft compounds and analysis of compound 1 a in the solid state shows inclusion of one molecule of CH(2)Cl(2) in the larger aromatic cleft, whereas in isomer 1 c disordered solvent molecules are trapped in the extended aromatic cleft. Furthermore, in the solid state, isomer 1 c forms infinite open channels along one of the crystallographic axes and perpendicular to this axis there are infinitely extending "wedged-ravines". Importantly, each of the diastereomers 1 a-c is resistant to inversion at the stereogenic nitrogen atoms under strongly and weakly acidic conditions in the range from room temperature (RT) to 95 degrees C. This observed configurational stability at the stereogenic nitrogens of 1 a-c is unique for analogues of Tröger's base in general to date. Finally, the ratio of cleft compounds 1 a and 1 c significantly increased relative to cavity compound 1 b when ammonium chloride was used as an additive in the Tröger's base condensation to 1 a-c suggesting a templating effect of the ammonium ion.

Absence of reverse anomeric effect in furanosides.

A series of conformationally restricted N-"furanosides" has been synthesized, where the carbons of the tetrahydrofuran ring are kept in one plane by a rigid norbornane skeleton, permitting only the ring oxygen to move above or below the tetrahydrofuran ring plane. This causes the substituents of the anomeric carbon to occupy a pseudoaxial or a pseudoequatorial position. On protonation of these "norbornane-furanosides" with trifluoromethanesulfonic acid, all three compounds exhibited decreasing coupling constants for the anomeric proton, indicating a shift toward the pseudoaxial conformation. The coupling constant measurements were supported by volume integration of NOESY cross-peaks, which also showed a change toward the pseudoaxial conformation upon protonation of the nitrogen. These results provide no evidence for the so-called reverse anomeric effect; on the contrary they are in full agreement with a small normal anomeric effect.