Adam M. Daly

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

Microwave measurements of proton tunneling and structural parameters for the propiolic acid–formic acid dimer

Microwave spectra of the propiolic acid-formic acid doubly hydrogen bonded complex were measured in the 1 GHz to 21 GHz range using four different Fourier transform spectrometers. Rotational spectra for seven isotopologues were obtained. For the parent isotopologue, a total of 138 a-dipole transitions and 28 b-dipole transitions were measured for which the a-dipole transitions exhibited splittings of a few MHz into pairs of lines and the b-type dipole transitions were split by ~580 MHz. The transitions assigned to this complex were fit to obtain rotational and distortion constants for both tunneling levels: A(0+) = 6005.289(8), B(0+) = 930.553(8), C(0+) = 803.9948(6) MHz, Δ(0+)(J) = 0.075(1), Δ(0+)(JK) = 0.71(1), and δ(0+)(j) = -0.010(1) kHz and A(0-) = 6005.275(8), B(0-) = 930.546(8), C(0-) = 803.9907(5) MHz, Δ(0-)(J) = 0.076(1), Δ(0-)(JK) = 0.70(2), and δ(0-)(j) = -0.008(1) kHz. Double resonance experiments were used on some transitions to verify assignments and to obtain splittings for cases when the b-dipole transitions were difficult to measure. The experimental difference in energy between the two tunneling states is 291.428(5) MHz for proton-proton exchange and 3.35(2) MHz for the deuterium-deuterium exchange. The vibration-rotation coupling constant between the two levels, F(ab), is 120.7(2) MHz for the proton-proton exchange. With one deuterium atom substituted in either of the hydrogen-bonding protons, the tunneling splittings were not observed for a-dipole transitions, supporting the assignment of the splitting to the concerted proton tunneling motion. The spectra were obtained using three Flygare-Balle type spectrometers and one chirped-pulse machine at the University of Virginia. Rotational constants and centrifugal distortion constants were obtained for HCOOH···HOOCCCH, H(13)COOH···HOOCCCH, HCOOD···HOOCCCH, HCOOH···DOOCCCH, HCOOD···DOOCCCH, DCOOH···HOOCCCH, and DCOOD···HOOCCCH. High-level ab initio calculations provided initial rotational constants for the complex, structural parameters, and some details of the proton tunneling potential energy surface. A least squares fit to the isotopic data reveals a planar structure that is slightly asymmetric in the OH distances. The formic OH···O propiolic hydrogen bond length is 1.8 Å and the propiolic OH···O formic hydrogen bond length is 1.6 Å, for the equilibrium configuration. The magnitude of the dipole moment was experimentally determined to be 1.95(3) × 10(-30) C m (0.584(8) D) for the 0(+) states and 1.92(5) × 10(-30) C m (0.576(14) D) for the 0(-) states.

Microwave spectrum, structural parameters, and quadrupole coupling for 1,2-dihydro-1,2-azaborine

The first microwave spectrum for 1,2-dihydro-1,2-azaborine has been measured in the frequency range 7-18 GHz, providing accurate rotational constants and nitrogen and boron quadrupole coupling strengths for three isotopomers, H(6)C(4)(11)B(14)N, H(6)C(4)(10)B(14)N, and H(5)DC(4)(11)B(14)N. The measured rotational constants were used to accurately determine coordinates for the substituted atoms and provide sufficient data to determine most of the important structural parameters for this molecule. The spectra were obtained using a pulsed beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of (14)N, (11)B, and (10)B nuclear quadrupole hyperfine interactions. High-level ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The rotational constants for the parent compound are A = 5657.335(1), B = 5349.2807(5), and C = 2749.1281(4) MHz, yielding the inertial defect Delta(0) = 0.02 amu x A(2) for the ground-state structure. The observed near-zero and positive inertial defect clearly indicates that the molecular structure of 1,2-dihydro-1,2-azaborine is planar. The least-squares fit analysis to determine the azaborine ring structure yielded the experimental bond lengths and 2sigma errors R(B-N) = 1.45(3) A, R(B-C) = 1.51(1) A, and R(N-C) = 1.37(3) A for the ground-state structure. Interbond angles for the ring were also determined. An extended Townes-Dailey population analysis of the boron and nitrogen quadrupole coupling constants provided the valence p-electron occupancy p(c) = 0.3e for boron and p(c) = 1.3e for nitrogen.

Laboratory characterization and astrophysical detection of vibrationally excited states of vinyl cyanide in Orion-KL

Context. We perform a laboratory characterization in the 18–1893 GHz range and astronomical detection between 80–280 GHz in Orion-KL with IRAM-30 m of CH2CHCN (vinyl cyanide) in its ground and vibrationally excited states. Aims. Our aim is to improve the understanding of rotational spectra of vibrationally excited vinyl cyanide with new laboratory data and analysis. The laboratory results allow searching for these excited state transitions in the Orion-KL line survey. Furthermore, rotational lines of CH2CHCN contribute to the understanding of the physical and chemical properties of the cloud. Methods. Laboratory measurements of CH2CHCN made on several different frequency-modulated spectrometers were combined into a single broadband 50–1900 GHz spectrum and its assignment was confirmed by Stark modulation spectra recorded in the 18–40 GHz region and by ab-initio anharmonic force field calculations. For analyzing the emission lines of vinyl cyanide detected in Orion-KL we used the excitation and radiative transfer code (MADEX) at LTE conditions. Results. Detailed characterization of laboratory spectra of CH2CHCN in nine different excited vibrational states: 11 = 1, 15 = 1, 11 = 2, 10 = 1 ⇔ (11 = 1,15 = 1), 11 = 3/15 = 2/14 = 1, (11 = 1,10 = 1) ⇔ (11 = 2,15 = 1), 9 = 1, (11 = 1,15 = 2) ⇔ (10 = 1,15 = 1) ⇔ (11 = 1,14 = 1), and 11 = 4 are determined, as well as the detection of transitions in the 11 = 2a nd 11 = 3 states for the first time in Orion-KL and of those in the 10 = 1 ⇔ (11 = 1,15 = 1) dyad of states for the first time in space. The rotational transitions of the ground state of this molecule emerge from four cloud components of hot core nature, which trace the physical and chemical conditions of high mass star forming regions in the Orion-KL Nebula. The lowest energy vibrationally excited states of vinyl cyanide, such as 11 = 1 (at 328.5 K), 15 = 1 (at 478.6 K), 11 = 2 (at 657.8 K), the 10 = 1 ⇔ (11 = 1,15 = 1) dyad (at 806.4/809.9 K), and 11 = 3 (at 987.9 K), are populated under warm and dense conditions, so they probe the hottest parts of the Orion-KL source. The vibrational temperatures derived for the 11 = 1, 11 = 2, and 15 = 1 states are 252 ± 76 K, 242 ± 121 K, and 227 ± 68 K, respectively; all of them are close to the mean kinetic temperature of the hot core component (210 K). The total column density of CH2CHCN in the ground state is (3.0 ± 0.9) × 10 15 cm −2 . We report the detection of methyl isocyanide (CH3NC) for the first time in Orion-KL and a tentative detection of vinyl isocyanide (CH2CHNC). We also give column density ratios between the cyanide and isocyanide isomers, obtaining a N(CH3NC)/N(CH3CN) ratio of 0.002. Conclusions. Laboratory characterization of many previously unassigned vibrationally excited states of vinyl cyanide ranging from microwave to THz frequencies allowed us to detect these molecular species in Orion-KL. Column density, rotational and vibrational temperatures for CH2CHCN in their ground and excited states, and the isotopologues have been constrained by means of a sample of more than 1000 lines in this survey.

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.

Communications: Evidence for proton tunneling from the microwave spectrum of the formic acid-propriolic acid dimer.

The microwave spectrum of the formic acid-propriolic acid dimer was measured in the 5-13 GHz range using a pulsed-beam, Fourier transform spectrometer. 22 a-dipole rotational transitions and 3 b-dipole rovibrational transitions were measured for the normal isotopomer. All of these observed transitions were split into doublets by the effects of the concerted tunneling of the two acid protons. The smaller splittings of 1-1.5 MHz for the a-dipole transitions are due to the differences in rotational constants for the upper and lower tunneling states. The b-dipole transitions are rovibrational (combination) transitions with a change in rotational state and tunneling state and provide direct information on the tunneling splittings since these observed splittings are the sum of the tunneling level splittings for the two rotational states involved in the transition. The b-dipole splittings are 55.16(0(00)-1(11)), 58.58(1(01)-2(12)), and 71.24 MHz(2(02)-3(13)). No similar splittings were observed when deuterium was substituted for either or both of the hydrogen bonding protons. For the lower tunneling state (nu(0) (+)), A=5988.7(7), B=927.782(7), and C=803.720(7) MHz. For the upper tunneling state (nu(0) (-)), A=5988(1), B=927.78(1), and C=804.06(1) MHz. Using a simple model with potential function V=ax(4)-bx(2) the splittings could be reproduced reasonably well with a barrier height of H(e)=3800 cm(-1).

Microwave measurements and ab initio calculations of structural and electronic properties of N-Et-1,2-azaborine.

Rotational transitions for N-Et-1,2-azaborine were measured in the 5-13 GHz range using a Flygare-Balle type Fourier transform spectrometer system. Twelve distinct rotational transitions with over 130 resolved hyperfine components, which included a-dipole and b-dipole transitions, were measured and analyzed to obtain rotational constants and (11)B and (14)N nuclear quadrupole coupling constants in the principal rotational axis system. Rotational constants obtained are A=4477.987(4), B=1490.5083(7), and C=1230.6728(6) MHz. The quadrupole coupling constants for (11)B are eQq(aa)=-1.82(1), (eQq(bb)-eQq(cc))=-3.398(4) MHz, and for (14)N, eQq(aa)=1.25(1), (eQq(bb)-eQq(cc))=0.662(4) MHz. Quantum electronic structure calculations predict a ground-state structure with the ethyl group perpendicular to the azaborine plane and rotational constants in very good agreement with the measured structure and rotational constants. The theoretical conformational analysis of the ethyl group rotation around the N[Single Bond]C bond in relation to the heterocyclic ring yielded an asymmetric torsional potential energy surface with barrier heights of about 900 and 1350 cm(-1) for the N-Et-1,2-azaborine. Results of the measurements and calculations indicate that the basic molecular structure of N-Et-1,2-azaborine is similar to ethylbenzene. Electrostatic potential calculations qualitatively show that pi-electron density is somewhat delocalized around the 1,2-azaborine ring.

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.

Gas phase measurements of mono-fluoro-benzoic acids and the dimer of 3-fluoro-benzoic acid

The microwave spectrum of the mono-fluoro-benzoic acids, 2-fluoro-, 3-fluoro-, and 4-fluoro-benzoic acid have been measured in the frequency range of 4-14 GHz using a pulsed beam Fourier transform microwave spectrometer. Measured rotational transition lines were assigned and fit using a rigid rotor Hamiltonian. Assignments were made for 3 conformers of 2-fluorobenzoic acid, 2 conformers of 3-fluorobenzoic acid, and 1 conformer of 4-fluorobenzoic acid. Additionally, the gas phase homodimer of 3-fluorobenzoic acid was detected, and the spectra showed evidence of proton tunneling. Experimental rotational constants are A(0(+)) = 1151.8(5), B(0(+)) = 100.3(5), C(0(+)) = 87.64(3) MHz and A(0(-)) = 1152.2(5), B(0(-)) = 100.7(5), C(0(-)) = 88.85(3) MHz for the two ground vibrational states split by the proton tunneling motion. The tunneling splitting (ΔE) is approximately 560 MHz. This homodimer appears to be the largest carboxylic acid dimer observed with F-T microwave spectroscopy.

Comprehensive Analysis of Prebiotic Propenal up to 660 GHz

Since interstellar detection of propenal is only based on two rotational transitions in the centimeter wave region, its high resolution rotational spectrum has been measured up to 660 GHz and fully characterized by assignment of more than 12,000 transitions to provide direct laboratory data to the astronomical community. Spectral assignments and analysis include transitions from the ground state of the trans and cis isomers, three trans-13C isotopologues, and ten excited vibrational states of the trans form. Combining new millimeter and submillimeter data with those from the far-infrared region has yielded the most precise set of spectroscopic constants of trans-propenal obtained to date. Newly determined rotational constants, centrifugal distortion constants, vibrational energies, and Coriolis and Fermi interaction constants are given with high accuracy and were used to predict transition frequencies and intensities over a wide frequency range. Results of this work should facilitate astronomers further observation of propenal in the interstellar medium.