Isabel Peña

Preferred conformers of proteinogenic glutamic acid.

The molecular shape of proteinogenic glutamic acid has been determined for the first time. Vaporization of the solid amino acid by laser ablation in combination with Fourier transform microwave spectroscopy made possible the detection of five different structures in a supersonic jet. These structures have been identified through their rotational and (14)N quadrupole coupling constants. All conformers show hydrogen bonds linking the amino and alpha carboxylic group through N-H···O═C (type I) or N···H-O (type II) interactions. In three of them there are additional hydrogen bonds established between the amino group and the carboxylic group in the gamma position. Entropic effects related to the side chain have been found to be significant in determining the most populated conformations.

All Five Forms of Cytosine Revealed in the Gas Phase

The determination of preferred tautomers of nucleobases has been of interest since the structure of nucleic acid and its base pairs was first reported. Molecular-level understanding of their structure can provide important insight into the relationship that exists between the presence of tautomeric forms and spontaneous mutation in DNA. The best experimental approach to address the structural preferences of nucleobases is to place them under isolation conditions in the gas phase, cooled in a supersonic expansion. Under these conditions, the various tautomers/conformers can coexist and are not affected by the bulk effects of their native environments, which normally mask their intrinsic molecular properties. The main restriction to the gas-phase study of these building blocks is the difficulty in their vaporization owing to their high melting points (ranging from 316 8C for guanine to 365 8C for adenine) and associated low vapor pressures. We have shown previously that the use of molecular beam Fourier transform microwave (MB-FTMW) spectroscopy in conjunction with laser ablation (LA) enables these vaporization problems to be overcome and renders the study of the rotational spectra of coded amino acids accessible. The success of these LA-MBFTMW experiments prompted their application to nucleic acids, and our initial studies on uracil and thymine enabled the determination of the structures of their diketo forms present in the gas phase. A subsequent study of guanine led us to unequivocally identify the four most stable tautomers in the gas phase. The molecular system of cytosine (CY) is even more complex than that of guanine. Figure 1a shows the five most stable species, in order of stability according to theoretical calculations: enol–amino trans (EAt), enol– amino cis (EAc), keto–amino (KA), keto–imino trans (KIt), keto–imino cis (KIc). In 1988, Szczesniak et al. observed the infrared spectra of CY isolated in inert Ar and N2 matrices and showed that isolated cytosine exists under these conditions as a mixture of the KA and EA forms (they did not distinguish between EAt and EAc). Brown et al. reported the free-jet millimeterwave absorption spectra of three species, which were tentatively assigned as the KA, EAt, and KI forms. The identification was based on the values of the rotational constants alone. In contrast, Dong and Miller used infrared laser spectroscopy in helium nanodroplets to characterize EAt, EAc, and KA species. Nir et al. attributed two features observed in the vibronic spectra to the KA and EA forms. The electron diffraction pattern was interpreted in terms of a conformation mixture dominated by the EA forms. X-ray photoemission spectra provide spectral signatures of oxo and hydroxy populations. In recent experiments in an Ar matrix, photoisomerization processes induced by narrowband tunable near-infrared and UV light were interpreted in terms of the existence of various tautomers of CY. No conclusive experimental evidence for the coexistence of the five predicted forms has yet been reported. We took advantage of the capabilities of LA-MB-FTMW spectroscopy to investigate the rotational spectra of cytosine in the solvent-free environment of a supersonic expansion. In this technique, the solid samples are vaporized by laser ablation, and the molecules are seeded in a supersonic expansion, in which CY is ideally frozen and the most stable forms trapped in their energy minima. The rotational spectrum of each of these molecular forms can be analyzed separately by Fourier transform microwave spectroscopy. Figure 1b shows details of the five 11,1–00,0 transitions corresponding to five different rotamers of CY observed in the 5100–5300 MHz frequency range. Each rotational transition shows a very complex hyperfine structure composed of tens of quadrupole component lines owing to the presence of three N nuclei. This hyperfine structure arises from the coupling of the N nuclear-spin angular momenta (I = 1) to the overall rotational angular momentum through the interaction of the quadrupole moment of each N nucleus with the electric-field gradient created at the site of this nucleus by the rest of the molecular charges. Analysis of this hyperfine structure yields the nuclear quadrupole coupling constants cab (a,b = a, b, c), which are extremely sensitive to the electronic distribution around the quadrupolar nuclei N1, N3, and N8 (see Figure 1a for nitrogen-atom labeling) and can be used as a valuable tool for the unambiguous identification of tautomers of CY. [*] Prof. J. L. Alonso, Dr. V. Vaquero, Dr. I. PeÇa, Prof. J. C. L pez, S. Mata, Prof. W. Caminati Grupo de Espectroscop a Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia Parque Cient fico UVa, Universidad de Valladolid 47005 Valladolid (Spain) E-mail: jlalonso@qf.uva.es Homepage: http://www.gem.uva.es [] Present address: Dipartimento di Chimica “G. Ciamician” dell’Universit via Selmi 2, 40126 Bologna (Italy)

The conformational behaviour of free D-glucose—at last

The conformational behaviour of isolated D-glucose has been revealed in this work using Fourier transform microwave spectroscopy coupled with laser ablation of crystalline α- and β-glucopyranose samples. Four conformers of α-D-glucopyranose and three of β-D-glucopyranose have been unequivocally identified on the basis of the spectroscopic rotational parameters in conjunction with ab initio predictions. Stereoelectronic hyperconjugative factors, like those associated with anomeric or gauche effects, as well as the cooperative OH⋯O chains extended along the entire molecule, are the main factors driving the conformational behaviour. The most abundant conformers exhibit a counter-clockwise arrangement (cc) of the network of intramolecular hydrogen bonds.

Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue

Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.

Six pyranoside forms of free 2-deoxy-D-ribose.

Carbohydrates are one of the most versatile biochemical building blocks, widely acting in energetic, structural, or recognition processes. The interpretation of the biological activity of saccharides is based on the structure and relative stability of their conformers. One of the obstacles to resolving the basic structure issues arises from their ability to form strong intermolecular hydrogen bonds with polar solvents, which in turn can result in conformational changes. A clear picture of the conformational panorama of isolated 2-deoxyd-ribose has been revealed using Fourier-transform microwave spectroscopy in conjunction with a UV ultrafast laser ablation source. Additionally, the availability of rotational data has been the main bottle-neck for examining the presence of these building blocks in interstellar space, so these studies could also be useful to the astrochemistry community. 2-Deoxy-d-ribose (2DR, C5H10O4; Figure 1a) is an important naturally occurring monosaccharide, present in nucleotides, which are the building blocks for DNA. In DNA, 2DR is present in the furanose (five-membered) ring form, whereas free in aqueous solution it cyclizes into fiveor six-membered rings, with the latter—the pyranoid form—being dominant. By closing the chain into a six-membered ring, the C1 carbon atom is converted into an asymmetric center, yielding two possible stereochemical a and b anomeric species (Figure 1b). In aqueous solution, 2DR primarily exists as a mixture of nearly equal amounts of a and b pyranose forms, present in their low-energy chair conformations, C1 and C4 (Figure 1c). [4] Such configurations are connected through ring inversion, thus establishing the axial or equatorial position of the OH group for each conformer. In addition, the monossacharides exhibit an unusual preferential stabilization of pyranose rings containing an axial OH group at the C1 carbon over the equatorial orientation, widely known as the anomeric effect, although its physical origin remains controversial. Nevertheless, structural analysis of 2DRmust take into consideration the intramolecular hydrogen bonding between adjacent OH groups. The formation of hydrogenbond networks reinforces their stability owing to hydrogenbond cooperativity effects. Such networks are fundamental to the molecular recognition of carbohydrates. By dissecting all these factors we can determine the most stable conformers of 2DR and the relative arrangement of the different hydroxy groups under isolated conditions, such as in the gas phase. In vacuo theoretical calculations, carried out on a-/bpyranoses, a-/b-furanoses, and open-chain conformations, predict 15 furanose and pyranose forms (Figure 1d, Table 1) in an energy window of 12 kJmol 1 above the predicted cc-apyr C1 global minimum. The notation used to label the different conformers include the symbols a and b to denote the anomer type, C1 and C4 to denote the pyranose chair form, C2-endo or C3-endo to denote the furanose envelope forms, and “c” or “cc” to indicate a clockwise or counterclockwise configuration of the adjacent OH bonds, respectively. A number is added to provide theMP2 energy ordering within the same family. To validate the predicted conformational behavior, comparison with precise experimental data of 2DR is needed. Previous experiments to determine the conformation of monosaccharides were based on X-ray and NMR measurements. However, these data are influenced by environmental effects associated with the solvent or crystal lattice. Recently, an IR spectrum of 2DR in an inert matrix in

Water–Water and Water–Solute Interactions in Microsolvated Organic Complexes†

A structural study of microsolvated clusters of β-propiolactone (BPL) formed in a pulsed molecular jet expansion is presented. The rotational spectra of BPL-(H2O)n (n=1-5) adducts have been analyzed by broadband microwave spectroscopy. Unambiguous identification of the structures has been achieved using isotopic substitution and experimental measurements of the cluster dipole moment. The observed structures are discussed in terms of the different intermolecular interactions between water molecules and between water and BPL, which include n-π* interactions involving the lone pairs of electrons on water oxygen atoms and the antibonding orbital of the BPL carbonyl group. The changes induced in the structures of the water hydrogen-bonding network by complexation to BPL indicate that water clusters adopt specific configurations to maximize their links to solute molecules.

LABORATORY AND ASTRONOMICAL DISCOVERY OF HYDROMAGNESIUM ISOCYANIDE

We report on the detection of hydromagnesium isocyanide, HMgNC, in the laboratory and in the carbon-rich evolved star IRC+10216. The J = 1-0 and J = 2-1 lines were observed in our microwave laboratory equipment in Valladolid with a spectral accuracy of 3 KHz. The hyperfine structure produced by the nitrogen atom was resolved for both transitions. The derived rotational constants from the laboratory data are B 0 = 5481.4333(6) MHz, D 0 = 2.90(8) KHz, and eQq(N) = –2.200(2) MHz. The predicted frequencies for the rotational transitions of HMgNC in the millimeter domain have an accuracy of 0.2-0.7 MHz. Four rotational lines of this species, J = 8-7, J = 10-9, J = 12-11, and J = 13-12, have been detected toward IRC+10216. The differences between observed and calculated frequencies are <0.5 MHz. The rotational constants derived from space frequencies are B 0 = 5481.49(3) MHz and D 0 = 3.2(1) KHz, i.e., identical to the laboratory ones. A merged fit to the laboratory and space frequencies provides B 0 = 5481.4336(4) MHz and D 0 = 2.94(5) KHz. We have derived a column density for HMgNC of (6 ± 2) × 1011 cm–2. From the observed line profiles the molecules have to be produced in the layer where other metal-isocyanides have been already found in this source. The abundance ratio between MgNC and its hydrogenated variety, HMgNC, is 20.

Disentangling the Puzzle of Hydrogen Bonding in Vitamin C.

Fast-passage Fourier transform microwave spectroscopy in combination with a laser ablation source has been successfully applied to probe vitamin C (l-ascorbic acid) in the gas phase. Its ethyldiol side chain and two hydroxyl groups around the γ-lactone ring provide five internal rotation axes, enabling vitamin C to assume a wide variety of nonplanar 3D cooperative hydrogen bond networks that can also include the keto and ether functions. The rotational constants extracted from the analysis of the spectrum unequivocally identify the existence of three dominant conformers stabilized by different intramolecular hydrogen bonding motifs forming five-, six-, or seven-membered rings.

Seven Conformers of Neutral Dopamine Revealed in the Gas Phase

The rotational spectrum of neutral dopamine has been investigated for the first time using a combination of Fourier transform microwave spectroscopy with laser ablation. The parameters extracted from the analysis of the spectrum unequivocally identify the existence of seven conformers of dopamine. (14)N nuclear quadrupole coupling interactions have been used to determine the orientation of the amino group probing the existence of stabilizing N-H···π interactions for all observed conformers.

Conformations of D-xylose: the pivotal role of the intramolecular hydrogen-bonding

Crystalline samples of D-xylose have been vaporized by laser ablation and probed in the gas phase using Fourier transform microwave spectroscopy. The rotational spectrum revealed the existence of two α-D-xylopyranose conformers stabilized by the anomeric effect and cooperative hydrogen bond networks. The experiment spectroscopically tracked fine structural changes upon clockwise and counterclockwise arrangements of the OH groups in the observed conformers. The five monosubstituted (13)C species of the most abundant conformer cc-α-(4)C1 have also been observed in their natural abundance, and its structure has been derived. This work demonstrates the pivotal role that the intramolecular hydrogen-bonding network plays in the conformational behavior of free monosaccharides.