Santiago Mata

Construction of a molecular beam Fourier transform microwave spectrometer used to study the 2,5-dihydrofuran-argon van der Waals complex

Abstract The rotational spectrum of the van der Waals complex consisting of argon and 2,5-dihydrofuran has been observed in a molecular beam Fourier transform microwave spectrometer in the frequency range 5–18.5 GHz. Analysis of the derived spectroscopic constants shows that the dimer has a structure with a plane of symmetry in which the argon atom is located 3.48 A above the ring plane. The experimental setup of the molecular beam Fourier transform microwave spectrometer is also presented.

A laser-ablation molecular-beam Fourier-transform microwave spectrometer: The rotational spectrum of organic solids

A spectrometer that combines laser ablation of a solid sample with molecular-beam Fourier-transform microwave spectroscopy (MB-FTMW) has been constructed to obtain the rotational spectrum of solid organic molecules. Laser ablation is produced by visible radiation, using the second harmonic of a Nd:YAG laser. The laser hits a solid rod placed on a specially designed pulsed nozzle, coaxially oriented with the axis of the microwave spectrometer Fabry–Perot cavity. The vaporized molecules are seeded in the supersonic jet formed by the expansion of a carrier gas (Ar,Ne) and probed by FTMW spectroscopy. The high sensitivity of the spectrometer is exemplified with the observation of minor isotopomers in natural abundance of different organic molecules and natural amino acids. This instrument opens perspectives in the investigation of the gas phase structure of solid organic compounds.

Conformations of γ‐Aminobutyric Acid (GABA): The Role of the n→π* Interaction

g-Aminobutyric acid (GABA) is arguably the most important inhibitory neurotransmitter in the brain and brainstem/spinal cord. Owing to the high torsional flexibility of its heavyatom backbone, this molecular system has a large number of low-energy conformers (see Figure 1). Identifying the stable conformers of GABA can be relevant to understanding the selectivity of the biological processes in which the neurotransmitter participates. This can be done by placing GABA on a supersonic jet such that conformers are cooled down and trapped in their energy minima. In such an isolated environment the conformers with sufficient population can be detected and studied by spectroscopic methods. In this context, several methods have made great contributions to the elucidation of the structures of biomolecules in the gas phase. In the present work we have observed and characterized nine conformers of GABA using Fourier transform microwave spectroscopy in supersonic jets combined with laser ablation. Microwave spectroscopy, considered the most definitive gas-phase structural probe, can distinguish between different conformational structures since they have unique moments of inertia and give separate rotational spectra. In general, large molecules, in particular those of biological importance, have low vapor pressures and tend to degrade upon heating, making them unsuited for structural studies in the gas phase. Recently, rotational studies of biomolecules have entered in a new stage with the LAMB-FTMW experiment, which combines laser ablation (LA) with molecular beam Fourier transform microwave spectroscopy (MB-FTMW), an approach that overcomes the problems of thermal decomposition associated with conventional heating methods. To date, different aand b-amino acids have been studied using this technique, making it possible to characterize their preferred conformations. Even in conformationally challenging systems these can be identified by rotational spectroscopy, as has been illustrated with the assignment of seven low-energy conformers of serine and threonine, six of cysteine, and four of b-alanine and proline. In the present work, we have examined the conformations of GABA. In this system the separation of the polar amino and carboxylic groups, characteristic of many families of neurotransmitters, opens new conformational possibilities with respect to a-amino acids if one considers the balance of intramolecular forces that contribute to stabilizing the different conformations. The five hindered rotations around the single bonds generate a plethora of conformational species (Figure 1). An overall picture of the conformational landscape obtained from theoretical predictions at the MP2/6-311++G(d,p) level confirms the conformational richness of GABA: the 30 feasible conformers shown in Figure 1 were localized with relative energies below 900 cm . These conformers are labeled by two letters (a, G, or g) followed by a number. The first letter refers to the configuration at Ca and the second one to the configuration at Cg : a means anti conformers, G gauche conformers with positive value of the torsional angle CCOOH-Ca-Cb-Cg or N-Cg-Cb-Ca, and g gauche conformers Figure 1. Predicted low-energy conformers of GABA. The nine observed conformers are circled.

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.

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

How water links to cis and trans peptidic groups: the rotational spectrum of N-methylformamide–water

We investigated the Fourier transform microwave spectra of the hydrated forms of N-methylformamide (NMF) in a supersonic expansion and assigned the rotational spectra of two mono-hydrated species. The conformation of each molecular complex was reliably determined on the basis of the values of the rotational constants, of the relative intensities of mu(a)- and mu(b)-type transitions, and of the features of the (14)N quadrupole hyperfine structure of the rotational transitions. In both complexes water acts as a proton donor and NMF has a trans configuration of the peptidic group. In the most stable of these conformers, water is also weakly bound to the methyl group.

A rotational study of laser ablated thiourea

A laser ablation device in combination with a molecular beam Fourier-transform microwave spectrometer has allowed the observation of the rotational spectrum of solid thiourea for the first time. The sensitivity reached in the experiment allowed the observation of the isotopomers (34)S, (13)C, and (15)N in their natural abundance. The spectrum of D(4)-thiourea was also analyzed from an enriched sample. The complicated hyperfine structure arising from the presence of two (14)N quadrupolar nuclei has been fully resolved and analyzed. The substitution r(s) structure has been derived from the experimental moments of inertia. Thiourea in gas phase presents a planar heavy atom skeleton. Experimental inertial defect values and high-level ab initio calculations reveal that the amino groups hydrogen atoms lie out-of-plane with a C(2) symmetry configuration and are involved in large amplitude inversion motions.

Jet-cooled rotational spectrum of laser-ablated 1,3,5-trithiane ☆

Abstract The jet-cooled rotational spectra of the parent and three isotopic species (13CC2H6S3, C3H634SS2 and C3H633SS2) in natural abundance of 1,3,5-trithiane have been observed by laser ablation combined with molecular-beam Fourier transform microwave spectroscopy. The r0 and rs structures of the molecule have been determined from the rotational data. The sensitivity of the experimental set-up proved to be high enough to observe the 33S isotopomer in natural abundance. An analysis of the nuclear quadrupole hyperfine structure due to the 33S nucleus allowed the determination of the quadrupole coupling tensor, giving some insight about the electronic distribution around this atom.

Tautomerism and microsolvation in 2-hydroxypyridine/2-pyridone.

The Fourier transform microwave spectra of the hydrated forms of the tautomeric pair 2-pyridinone/2-hydroxypyridine (2PO/2HP) have been investigated in a supersonic expansion. Three hydrated species, 2PO-H₂O, 2HP-H₂O, and 2PO-(H₂O)₂, have been observed in the rotational spectrum. Each molecular complex was confidently identified by the features of the ¹⁴N quadrupole hyperfine structure of the rotational transitions. The presence of water affects the tautomeric equilibrium -N═C(OH)- ↔ -NH-C(═O)-, which is shifted to the enol form for the bare molecules 2PO/2HP but to the keto tautomer for the hydrated forms.