Conformationally Restricted ß-Sheet Breaker Peptides Incorporating Cyclic α-Methylisoserine Sulfamidates.

Peptides containing variations of the ß-amyloid hydrophobic core and five-membered sulfamidates derived from ß-amino acid α-methylisoserine have been synthesized and fully characterized in the gas phase, solid state and in aqueous solution by a combination of experimental and computational techniques. The cyclic sulfamidate group effectively locks the secondary structure at the N-terminus of such hybrid peptides imposing a conformational restriction and stabilizing non-extended structures. This conformational bias, which is maintained in the gas phase, solid state and aqueous solution, is shown to be resistant to structure templating through assays of in vitro ß-amyloid aggregation, acting as ß-sheet breaker peptides with moderate activity.

Bond Length Alternation and Internal Dynamics in Model Aromatic Substituents of Lignin.

Broadband microwave spectra were recorded over the 2-18 GHz frequency range for a series of four model aromatic components of lignin; namely, guaiacol (ortho-methoxy phenol, G), syringol (2,6-dimethoxy phenol, S), 4-methyl guaiacol (MG), and 4-vinyl guaiacol (VG), under jet-cooled conditions in the gas phase. Using a combination of 13 C isotopic data and electronic structure calculations, distortions of the phenyl ring by the substituents on the ring are identified. In all four molecules, the rC(1)-C(6) bond between the two substituted C-atoms lengthens, leading to clear bond alternation that reflects an increase in the phenyl ring resonance structure with double bonds at rC(1)-C(2) , rC(3)-C(4) and rC(5)-C(6) . Syringol, with its symmetric methoxy substituents, possesses a microwave spectrum with tunneling doublets in the a-type transitions associated with H-atom tunneling. These splittings were fit to determine a barrier to hindered rotation of the OH group of 1975 cm-1 , a value nearly 50 % greater than that in phenol, due to the presence of the intramolecular OH⋅⋅⋅OCH3 H-bonds at the two equivalent planar geometries. In 4-methyl guaiacol, methyl rotor splittings are observed and used to confirm and refine an earlier measurement of the three-fold barrier V3 =67 cm-1 . Finally, 4-vinyl guaiacol shows transitions due to two conformers differing in the relative orientations of the vinyl and OH groups.

The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane.

The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.

Bond Length Alternation Observed Experimentally: The Case of 1H-Indazole.

Bond length alternation is a chemical phenomenon in benzene rings fused to other rings, which has been mainly predicted theoretically. Its physical origin is still not clear and has generated discussion. Here, by using a strategy that combines microwave spectroscopy, custom-made synthesis and high-level ab initio calculations, we demonstrate that this phenomenon is clearly observed in the prototype indazole molecule isolated in the gas phase. The 1H-indazole conformer was detected by rotational spectroscopy, and its 17 isotopologues resulting from single and double heavy atom substitution (13 C and 15 N) were also unambiguously observed. Several experimental structures were determined and, in particular, the most useful semi-experimental equilibrium structure (re SE ), allowed determination of the heavy atom bond lengths to milli-Ångstrom precision. The experimentally determined bond length alternation is estimated to correspond to 60:40 contributions from the two resonant forms of 1H-indazole.

Interactions between azines and alcohols: a rotational study of pyridine-tert-butyl alcohol.

We assigned the rotational spectra of the parent and the OD isotopologues of the intermolecular complex pyridine-tert-butyl alcohol. The rotational and 14N quadrupole coupling constants are in agreement with a σ-type shape and a Cs symmetry of the complex. The two subunits are held together by a "classical" O-HN intermolecular hydrogen bond. Structural features of these hydrogen bonds are given and compared to those of similar molecular adducts. The ON distance decreases by 4 mÅ upon deuteration of the hydroxyl group, denoting a marked reverse Ubbelohde effect of the O-HN hydrogen bond.

A General Treatment to Study Molecular Complexes Stabilized by Hydrogen-, Halogen-, and Carbon-Bond Networks: Experiment and Theory of (CH2 F2 )n ⋠⋠⋠(H2 O)m.

Rotational spectra of several difluoromethane-water adducts have been observed using two broadband chirped-pulse Fourier-transform microwave (CP-FTMW) spectrometers. The experimental structures of (CH2 F2 )⋅⋅⋅(H2 O)2 , (CH2 F2 )2 ⋅⋅⋅(H2 O), (CH2 F2 )⋅⋅⋅(H2 O)3 , and (CH2 F2 )2 ⋅⋅⋅(H2 O)2 were unambiguously identified with the aid of 18 isotopic substituted species. A subtle competition between hydrogen, halogen, and carbon bonds is observed and a detailed analysis was performed on the complex network of non-covalent interactions which stabilize each cluster. The study shows that the combination of stabilizing contact networks is able to reinforce the interaction strength through a cooperative effect, which can lead to large stable oligomers.

Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition.

The tumor-associated carbohydrate Tn antigens include two variants, αGalNAc- O-Thr and αGalNAc- O-Ser. In solution, they exhibit dissimilar shapes and dynamics and bind differently to the same protein receptor. Here, we demonstrate experimentally and theoretically that their conformational preferences in the gas phase are highly similar, revealing the essential role of water. We propose that water molecules prompt the rotation around the glycosidic linkage in the threonine derivative, shielding its hydrophobic methyl group and allowing an optimal solvation of the polar region of the antigen. The unusual arrangement of αGalNAc- O-Thr features a water molecule bound into a "pocket" between the sugar and the threonine. This mechanism is supported by trapping, for the first time, such localized water in the crystal structures of an antibody bound to two glycopeptides that comprise fluorinated Tn antigens in their structure. According to several reported X-ray structures, installing oxygenated amino acids in specific regions of the receptor capable of displacing the bridging water molecule to the bulk-solvent may facilitate the molecular recognition of the Tn antigen with threonine. Overall, our data also explain how water fine-tunes the 3D structure features of similar molecules, which in turn are behind their distinct biological activities.

Investigating the Conformation of the Bridged Monosaccharide Levoglucosan.

Levoglucosan is one of the main products of the thermal degradation of glucose and cellulose and is commonly used as a tracer for biomass burning. Herein we report a conformational analysis of levoglucosan under isolation conditions, by means of microwave spectroscopy coupled with ultrafast laser vaporization in supersonic expansions. We observed three different conformations of levoglucosan in the gas phase. They all share a common heavy atom rigid bicyclic structure. The difference between the three of them lies in the network of intramolecular hydrogen bonds that arises from the OH groups at positions 2, 3 and 4. The different combinations of H-bonds give richness to the conformational landscape of levoglucosan. The gas phase conformers obtained in this work are compared to the crystal structure of levoglucosan previously reported. Although the heavy atom frame remains unchanged, there are significant differences in the positions of the H-atoms. In addition, the levoglucosan structure can be compared to the related glucose, for which gas phase conformational studies exist in the literature. In this case, in going from glucose to levoglucosan, there is an inversion in the chair conformation of the pyranose ring. This forces the OH groups to adopt axial positions (instead of the more favorable equatorial positions in glucose) and completely changes the pattern of intramolecular H-bonds.

Effects of Chlorination on the Tautomeric Equilibrium of 2-Hydroxypyridine: Experiment and Theory.

The effects of halogenation on the tautomeric and conformational equilibria of the model system 2-hydroxypyridine/2-pyridone have been investigated through chlorine substitution at positions 3, 4, 5, and 6. In the gas phase, the lactim syn-periplanar tautomer (OHs ) was the predominant species for all compounds over the lactam form (C=O) and the less abundant anti-periplanar lactim (OHa ). However, the population of the three species was shown to be dependent on the position of the chlorine substitution. Chlorination in position 5 or 6 strongly stabilizes the OHs tautomer, whereas the C=O form has a significant population when the ring is chlorinated in positions 3 or 4. Overall, the OHa form is the least favourable form, although the 3-substitution favours the population of this tautomer. In addition, the C=O tautomer is strongly stabilized in the solvent, which makes it the dominant form in some substituted species. This study has been performed by means of rotational spectroscopy in the gas phase and/or theoretical calculations in the isolated phase and in solution. Both the OHs and C=O forms of 5-chloro-2-hydroxypyridine and the OHs form of 6-chloro-2-hydroxypyridine were experimentally observed. All transitions displayed a complex nuclear hyperfine structure owing to the presence of the chlorine and nitrogen nuclei. For all species, a full quadrupolar hyperfine analysis has been performed. This has provided crucial information for the unambiguous identification of tautomers.

N-Methyl Inversion and Accurate Equilibrium Structures in Alkaloids: Pseudopelletierine.

A rotational spectroscopy investigation has resolved the conformational equilibrium and structural properties of the alkaloid pseudopelletierine. Two different conformers, which originate from inversion of the N-methyl group from an axial to an equatorial position, have been unambiguously identified in the gas phase, and nine independent isotopologues have been recorded by Fourier-transform microwave spectroscopy in a jet expansion. Both conformers share a chair-chair configuration of the two bridged six-membered rings. The conformational equilibrium is displaced towards the axial form, with a relative population in the supersonic jet of Naxial /Nequatorial ≈2/1. An accurate equilibrium structure has been determined by using the semiexperimental mixed-estimation method and alternatively computed by quantum-chemical methods up to the coupled-cluster level of theory. A comparison with the N-methyl inversion equilibria in related tropanes is also presented.

Structural Studies of Nicotinoids: Cotinine versus Nicotine.

Nicotinoids are agonists of the acetylcholine receptor (nAChR) and play important biochemical and pharmacological roles. Herein, we report on the structure and conformation of cotinine, and compare its molecular properties with the nicotine prototype, from which it only differs in the addition of a carbonyl group. This investigation included a theoretical survey of the effects of rotamerization of the pyridine moiety, the puckering of the pyrrolidinone ring and the internal rotation of the methyl group. The experimental work examined the rotational spectrum of the molecule in a supersonic expansion, using both broadband chirped-pulse excitation techniques and cavity microwave spectrometers. Two conformers were observed for cotinine, and the fine and hyperfine structures arising from the two quadrupolar 14 N nuclei and the methyl internal rotor were fully analyzed. The two observed conformers share the same twisted conformation of the five-membered ring, but differ in a roughly 180° rotamerization around the C-C bond connecting the two rings. The energy barriers for the internal rotation of the methyl group in cotinine (4.55(4) and 4.64(3) kJ mol-1 , respectively) are much lower than in nicotine (estimated in 16.5 kJ mol-1 ). The combination of different intramolecular electronic effects, hydrogen bonding and possible binding differences to receptor molecules arising from the carbonyl group could explain the lower affinity of cotinine for nAChRs.

Sensing the anomeric effect in a solvent-free environment.

The anomeric effect is a chemical phenomenon that refers to an observed stabilization of six-membered carbohydrate rings when they contain an electronegative substituent at the C1 position of the ring. This stereoelectronic effect influences the three-dimensional shapes of many biological molecules. It can be manifested not only in this classical manner involving interaction of the endocyclic oxygen atom (O5) found in such sugars with the C1 substituent (endo-anomeric effect) but also through a corresponding interaction of the electronegative exocyclic substituent with O5 (exo-anomeric effect). However, the underlying physical origin(s) of this phenomenon is still not clear. Here we show, using a combination of laser spectroscopy and computational analysis, that a truncated peptide motif can engage the two anomers of an isolated sugar in the gas phase, an environment lacking extraneous factors which could confound the analysis. (Anomers are isomers that differ in the orientation of the substituent at C1.) Complexes formed between the peptide and the α- or ß-anomers of d-galactose are nearly identical structurally; however, the strength of the polarization of their interactions with the peptide differs greatly. Natural bond order calculations support this observation, and together they reveal the dominance of the exo- over the endo-anomeric effect. As interactions between oxygen atoms at positions C1 and C2 (O1 and O2, respectively) on the pyranose ring can alter the exo/endo ratio of a carbohydrate, our results suggest that it will be important to re-evaluate the influence, and biological effects, of substituents at position C2 in sugars.

The Conformational Map of Volatile Anesthetics: Enflurane Revisited.

Previous ambiguities in the conformational and structural landscape of the volatile anesthetic enflurane have been solved combining microwave spectroscopy in a jet expansion and ab initio calculations. The broadband (2-18 GHz) rotational spectra identified three different rotamers, sharing a common trans ether skeleton but differing in the ±gauche/trans position of the terminal chlorine atom. For each chlorine conformation two different gauche orientations were predicted for the opposite difluoromethyl group, but only one is experimentally observable due to collisional relaxation in the jet. The experimental dataset comprised nine different isotopologues ((35) Cl, (37) Cl, (13) C) and a large number (>6500) of rotational transitions. The inertial data provided structural information using the substitution and effective procedures. The structural preferences were rationalized with additional ab initio, natural-bond-orbital and non-covalent-interaction analysis, which suggest that plausible anomeric effects at the difluoromethyl group could be overridden by other intramolecular effects. The difluoromethyl orientation thus reflects a minimization of inter-fluorine repulsions while maximizing F⋅⋅⋅H attractive interactions. A comparison with previous electron diffraction and spectroscopic data in the gas and condensed phases finally resulted in a comprehensive description of this ether, completing a rotational description of the most common multi-halogenated anesthetics.

Scopine Isolated in the Gas Phase.

The rotational spectrum of the tropane alkaloid scopine is detected by Fourier transform microwave spectroscopy in a pulsed supersonic jet. A nonconventional method for bringing the molecules intact into the gas phase is used in which scopine syrup is mixed with glycine powder and the solid mixture is vaporized with an ultrafast UV laser beam. Laser vaporization prevents the easy isomerization to scopoline previously observed with conventional heating methods. A single conformer is unambiguously observed in the supersonic jet and corresponds to the energetically most stable species according to quantum chemical calculations. Rotational and centrifugal distortion constants are accurately determined. The spectrum shows fine and hyperfine structure due to the hindered rotation of the methyl group and the presence of a quadrupolar nucleus (14 N), respectively. This additional information allows the angle of N-methyl inversion between the N-CH3 bond and the bicyclic C-N-C plane to be determined (131.8-137.8°), as well as the internal rotation barrier of the methyl group (6.235(1) kJ mol-1 ).

Modeling the tyrosine-sugar interactions in supersonic expansions: glucopyranose-phenol clusters.

Sugars are fundamental building blocks for living organisms and their interaction with proteins plays a central role in fundamental biological processes, such as energy storage and production, post-transductional modifications or immune response. Understanding those processes require deep knowledge of the forces that drive the interactions at the molecular level. Here we explore the interactions between α/ß-methyl-d-glucopyranose and ß-phenyl-d-glucopyranose with phenol, and the chromophore of tyrosine, using a combination of mass-resolved laser electronic spectroscopy in supersonic expansions and quantum mechanical calculations. The structures of the complexes detected in the jet are stabilized by a subtle equilibrium between several types of weak interactions, among which the dispersion forces may tilt the balance. In particular, the small structural changes introduced by the orientation of the anomeric substituent are amplified by the interaction with phenol. Consequently, the number of conformational isomers detected experimentally is different for each system and they present also differences in the preferred solvation site. Furthermore, inclusion of entropic terms for the calculated structures is advisable to understand the energetic reasons for the detection of a small set of experimental conformational isomers.

The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations.

Fructose and deoxyribose (24 and 19 atoms, respectively) are too large for determining accurate equilibrium structures, either by high-level ab initio methods or by experiments alone. We show in this work that the semiexperimental (SE) mixed estimation (ME) method offers a valuable alternative for equilibrium structure determinations in moderate-sized molecules such as these monosaccharides or other biochemical building blocks. The SE/ME method proceeds by fitting experimental rotational data for a number of isotopologues, which have been corrected with theoretical vibration-rotation interaction parameters (αi), and predicate observations for the structure. The derived SE constants are later supplemented by carefully chosen structural parameters from medium level ab initio calculations, including those for hydrogen atoms. The combined data are then used in a weighted least-squares fit to determine an equilibrium structure (r). We applied the ME method here to fructose and 2-deoxyribose and checked the accuracy of the calculations for 2-deoxyribose against the high level ab initio r structure fully optimized at the CCSD(T) level. We show that the ME method allows determining a complete and reliable equilibrium structure for relatively large molecules, even when experimental rotational information includes a limited number of isotopologues. With a moderate computational cost the ME method could be applied to larger molecules, thereby improving the structural evidence for subtle orbital interactions such as the anomeric effect.

Potential energy surface of fluoroxene: experiment and theory.

The potential energy surface (PES) of the general anesthetic fluoroxene (2,2,2-trifluoroethyl vinyl ether) was probed in a supersonic jet expansion using broadband chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy and theoretical calculations. The PES is dominated by a single conformation, as other stable minima are shown to kinetically relax in the expansion to the global minimum. Consistently, the rotational spectrum reveals a single conformation. Fluoroxene adopts a CS heavy-atom planar skeleton structure in the gas phase, with a cis-trans conformation (cis for the CH2=CH-O-CH2- and trans for the =CH-O-CH2-CF3 part). The sensitivity of a recently-built CP-FTMW spectrometer at the UPV/EHU is demonstrated by the detection of five isotopologues of fluoroxene in natural abundance, corresponding to the (13)C and (18)O monosubstituted species. The rS and r0 structures were determined and are in good agreement with theoretical predictions using the MP2, B3LYP and M06-2X methods.

Carbohydrates.

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

Internal dynamics in halogen-bonded adducts: a rotational study of chlorotrifluoromethane-formaldehyde.

The rotational spectra of two isotopologues of the 1:1 complex between chlorotrifluoromethane and formaldehyde have been recorded and analyzed by using Fourier-transform microwave spectroscopy. Only one rotamer was detected, with the two constituent molecules held together through a Cl⋅⋅⋅O halogen bond (R(Cl⋅⋅⋅O) = 3.048 Å). The dimer displays two simultaneous large-amplitude intramolecular motions. The internal rotation of formaldehyde around its symmetry axis (V2 = 28(5) cm(-1)) splits all the rotational transitions into two component lines with a relative intensity ratio of 1:3. On the other hand, the almost free internal rotation (V3 ≈ 2.5 cm(-1)) of the CF3 symmetric top increases the "rigid" value of the rotational constant A by almost one order of magnitude. In addition, all the transitions display a hyperfine structure due to the (35)Cl (or (37)Cl) nucleus quadrupole effects.

Structural distortion of the epoxy groups in norbornanes: a rotational study of exo-2,3-epoxynorbornane.

Exo-2,3-epoxynorbornane is studied in the gas phase by pulsed jet Fourier transform microwave spectroscopy in the 4-18 GHz region. Six isotopologues were observed and characterized in their natural abundance. The experimental substitution and effective structures were obtained. Comparison with the structure of norbornane shows significant differences in several bond lengths and valence angles upon introduction of the epoxy group. All the work is supported by quantum chemical calculations.