Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars.

The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (ß-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural ßf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural ßf. Unnatural αp and ßp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of ßf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in ßf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.

Conformational Behavior of d-Lyxose in Gas and Solution Phases by Rotational and NMR Spectroscopies.

Understanding the conformational preferences of carbohydrates is crucial to explain the interactions with their biological targets and to improve their use as therapeutic agents. We present experimental data resolving the conformational landscape of the monosaccharide d-lyxose, for which quantum mechanical (QM) calculations offer model-dependent results. This study compares the structural preferences in the gas phase, determined by rotational spectroscopy, with those in solution, resolved by nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations. In contrast to QM calculations, d-lyxose adopts only pyranose forms in the gas phase, with the α-anomer exhibiting both the 4C1 and 1C4 chairs (60:40). The predominantly populated ß-anomer shows the 4C1 form exclusively, as determined experimentally by isotopic substitution. In aqueous solution, the pyranose forms are also dominant. However, in contrast to the gas phase, the α-anomer as 1C4 chair is the most populated, and its solvation is more effective than for the ß derivative. Markedly, the main conformers found in the gas phase and solution are characterized by the lack of the stabilizing anomeric effect. From a mechanistic perspective, both rotational spectroscopy and solid-state nuclear magnetic resonance (NMR) corroborate that αâ€¯â†”â€¯ß or furanose ↔ pyranose interconversions are prevented in the gas phase. Combining microwave (MW) and NMR results provides a powerful method for unraveling the water role in the conformational preferences of challenging molecules, such as flexible monosaccharides.

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.

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 ).

Chiral recognition and atropisomerism in the sevoflurane dimer.

We have examined the stereoselectivity of molecular recognition between two molecules of the anesthetic sevoflurane using broadband rotational spectroscopy. The transient axial chirality of sevoflurane is revealed upon the formation of the dimer, as two different diastereoisomers made of either homo- or heterochiral species are detected in a supersonic jet expansion. The conformational assignment was confirmed by the observation of eighteen different isotopologues in natural abundance (all possible (13)C's and two (18)O species of the homochiral form). The two clusters are formed in practically equal proportions (1.1 : 1), probably due to their similar hydrogen bonding topologies. In both clusters the complex is stabilized by a primary C-H···O hydrogen bond, assisted by weak C-HF interactions. This intermolecular binding regime is characterized by a mixture of electrostatic and dispersive interactions, midway between classical hydrogen bonds and van der Waals clusters.

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.

Pseudorotational landscape of seven-membered rings: the most stable chair and twist-boat conformers of ε-caprolactone.

The conformational landscape and ring-puckering properties of ε-caprolactone have been analyzed by using microwave spectroscopy and quantum chemical calculations. Two conformers were detected in a supersonic jet expansion, the most stable form being a chair containing the ester group in its rectangular flap. This conformation benefits from reduced CH2 bond eclipsing and angle strain, while π-electron delocalization in the ester group is increased. The derived effective structure of the chair form satisfactorily agrees with the calculated near-equilibrium structure. A twist-boat conformer was also identified (9.4 kJ mol(-1) higher in energy at CCSD(T)/aug-cc-pVTZ level), and was located in the boat-twist-boat pseudorotation cycle of the seven-membered ring. Three other low-energy conformers were investigated and characterized in terms of the four puckering coordinates of the seven-membered ring. Potential interconversions in the four-dimensional conformation space are also discussed.

Competition between weak hydrogen bonds: C-H···Cl is preferred to C-H···F in CH2ClF-H2CO, as revealed by rotational spectroscopy.

We recorded the pulsed jet Fourier transform microwave spectrum of the 1 : 1 adduct of CH2ClF with formaldehyde. Formaldehyde is linked to CH2ClF through a C-H···Cl bond rather than a weak C-H···F hydrogen bond, with a H···Cl "bond length" of 2.918 Å. Two additional equivalent C-H···O contacts, with a H···O distance of 2.821 Å, characterize the complex. Tunnelling splittings due to the internal rotation of the formaldehyde moiety have been observed, which allowed estimating the barrier to the internal rotation of formaldehyde to be 125(10) cm(-1). The (35)Cl quadrupole coupling constants have been determined to be χaa = 31.131(7) MHz and χbb-χcc = -105.82(1) MHz.

O-H⋠⋠⋠N and C-H⋠⋠⋠O hydrogen bonds control hydration of pivotal tropane alkaloids: tropinone⋠⋠⋠H(2)O complex.

The effect of monohydration in equatorial/axial isomerism of the common motif of tropane alkaloids is investigated in a supersonic expansion by using Fourier-transform microwave spectroscopy. The rotational spectrum reveals the equatorial isomer as the dominant species in the tropinone⋅⋅⋅H2 O complex. The monohydrated complex is stabilized primarily by a moderate OH⋅⋅⋅N hydrogen bond. In addition, two CH⋅⋅⋅O weak hydrogen bonds also support this structure, blocking the water molecule and avoiding any molecular dynamics in the complex. The water molecule acts as proton donor and chooses the ternary amine group over the carbonyl group as a proton acceptor. The experimental work is supported by theoretical calculations; the accuracy of the B3LYP, M06-2X, and MP2 methods is also discussed.

Interactions between alkanes and aromatic molecules: a rotational study of pyridine-methane.

The rotational spectrum of the adduct pyridine-methane shows that methane links to an aromatic molecule apparently through a C-H···π weak hydrogen bond. The shape and the internal dynamics behaviour of this complex are very similar to that of the van der Waals complexes involving aromatic molecules with rare gases.

Interactions between freons: a rotational study of CH2F2-CH2Cl2.

The rotational spectra of two isotopologues of a 1:1 difluoromethane-dichloromethane complex have been investigated by pulsed-jet Fourier-transform microwave spectroscopy. The assigned (most stable) isomer has C(s) symmetry and it displays a network of two C-H⋅⋅⋅Cl-C and one C-H⋅⋅⋅F-C weak hydrogen bonds, thus suggesting that the former interactions are stronger. The hyperfine structures owing to (35)Cl (or (37)Cl) quadrupolar effects have been fully resolved, thus leading to an accurate determination of the three diagonal (χ(gg); g=a, b, c) and the three mixed quadrupole coupling constants (χ(gg'); g, g'=a, b, c; g≠g'). Information on the structural parameters of the hydrogen bonds has been obtained. The dissociation energy of the complex has been estimated to be 7.6 kJ mol(-1).

Probing the C-H⋠⋠⋠π weak hydrogen bond in anesthetic binding: the sevoflurane-benzene cluster.

Cooperativity between weak hydrogen bonds can be revealed in molecular clusters isolated in the gas phase. Here we examine the structure, internal dynamics, and origin of the weak intermolecular forces between sevoflurane and a benzene molecule, using multi-isotopic broadband rotational spectra. This heterodimer is held together by a primary C-H⋅⋅⋅π hydrogen bond, assisted by multiple weak C-H⋅⋅⋅F interactions. The multiple nonbonding forces hinder the internal rotation of benzene around the isopropyl C-H bond in sevoflurane, producing detectable quantum tunneling effects in the rotational spectrum.

Fluorination effects on the shapes of complexes of water with ethers: a rotational study of trifluoroanisole-water.

The rotational spectra of five isotopologues of the 1:1 complex trifluoroanisole-water have been investigated with pulsed jet Fourier transform microwave spectroscopy. The triple fluorination of the methyl group greatly affects the features of the rotational spectrum of the complex with water, with respect to those of the related complex anisole-water. The shape, the internal dynamics, and the isotopic effects turned out to be quite different from those of the anisole-water adduct ( Giuliano , B. M. ; Caminati , W. Angew. Chem., Int. Ed. 2005 , 44 , 603 - 606 ). However, as in anisole-water, water has the double role as a proton donor and proton acceptor, and it is linked to trifluoroanisole through two, O-H···O and C-H···O hydrogen bonds.

How water interacts with halogenated anesthetics: the rotational spectrum of isoflurane-water.

The rotational spectra of several isotopologues of the 1:1 complex between the inhaled anesthetic isoflurane and water have been recorded and analyzed by using Fourier transform microwave spectroscopy. The rotational spectrum showed a single rotamer, corresponding to the configuration in which the most stable conformer of isolated isoflurane is linked to the water molecule through an almost linear C-H⋅⋅⋅O weak hydrogen bond. All transitions display a hyperfine structure due to the (35)Cl (or (37)Cl) nuclear quadrupole effects.

Weak C-H···N and C-H···F hydrogen bonds and internal rotation in pyridine-CH3F.

The pulsed-jet Fourier transform rotational spectra of 4 isotopologues have been recorded for the most stable conformation of the molecular cluster pyridine-CH3F. Two weak C-H···N and C-H···F hydrogen bonds link the two subunits of the complex. Structural information on the hydrogen bridges has been obtained. The internal rotation of the CH3F subunit around its symmetry axis splits all rotational transitions into two (A and E) well resolved component lines, leading to a V3 barrier height of 1.55(1) kJ mol(-1).

Rotational spectra of bicyclic decanes: the trans conformation of (-)-lupinine.

The conformational and structural properties of the bicyclic quinolizidine alkaloid (-)-lupinine have been investigated in a supersonic jet expansion using microwave spectroscopy. The rotational spectrum is consistent with a single dominant trans conformation within a double-chair skeleton, which is stabilized by more than 10.4 kJ mol(-1) with respect to other conformations. In the isolated conditions of the jet, the hydroxy methyl side chain of the molecule locks in to form an intramolecular O-H···N hydrogen bond to the electron lone pair at the nitrogen atom. Accurate rotational constants, centrifugal distortion corrections, and (14)N nuclear quadrupole coupling parameters are reported and compared to ab initio (MP2) and DFT (M06-2X) calculations. The stability of lupinine is further compared computationally with epilupinine and decaline in order to gauge the influence of intramolecular hydrogen bonding, absent in these molecules.

Non-bonding interactions and internal dynamics in CH2F2···H2CO: a rotational and model calculations study.

The rotational spectra of three isotopologues of the 1 : 1 complex between difluoromethane and formaldehyde have been observed and assigned using pulsed jet Fourier transform microwave spectroscopy. The formaldehyde lies in the FCF plane of difluoromethane, linked through a C-H···F and a bifurcated CH2···O weak hydrogen bonds. The rotational transitions are split into two component lines with a relative intensity ratio of 1 : 3, due to the internal rotation of the formaldehyde moiety along its symmetry axis. The barrier to this motion has been estimated by using a flexible model to be V2 = 180(10) cm(-1).