H. Wieser

Infrared spectra: intramolecular trans lone pair interaction with α-CH bonds and the stability of conformers in alcohols and thiols

Abstract Doublet v(OH) bands in simple aliphatic alcohols due to rotational isomerism about the C-O bond are related to the number of α-CH bonds trans to an oxygen, lone pair orbital. v(OH) increases and v(α-OH) decreases when this condition is met. These frequency shifts can be rationalized by the participation of the oxygen lone pair in a σ* C-H orbital on the adjacent carbon, an interaction which appears to confer some stability on that conformer. This may be a significant factor governing rotational isomer populations in alcohols (and thiols). Specific studies of CH3CD2OH, (CH3)2CDOH and (CH3)2CDSH are reported. In aliphatic thiols the partial lone pair delocalization is found to be less significant, the overall order being N > O > S.

The vapor phase far‐infrared spectra of 1H‐indene, benzo[b]furan, 1,3,2‐benzodioxaborole, and indole: Evidence for planar skeletons and kinetic anharmonicity in the out‐of‐plane ring deformations

The far‐infrared spectra of the vapors of 1H‐indene, benzo[b]furan, 1, 3, 2‐benzodioxaborole (catechol borane), and indole are reported in the region of 100–500 cm−1. The spectra of the first three compounds exhibit series of C‐type Q branches for the three out‐of‐plane ring deformations, establishing planar skeletal configurations and indicating that the aromatic skeletons are not truly rigid. The lower of these two sequences are assigned as interlocking transitions arising from the deformation of the five‐membered ring and the butterfly mode, and are analyzed by means of a two‐dimensional Hamiltonian which includes for each mode a quadratic potential constant and a quadratic dependence of the reduced mass on each displacement coordinate, as well as a potential constant coupling the two modes.

1,3-benzodioxole: far-infrared spectrum 50–500 cm−1

Abstract The far-infrared spectrum of the vapour of 1,3-benzodioxole in the region of 50–500 cm −1 is reported and interpreted in terms of combination and interstate transitions involving four skeletal deformations. Analysis of the out-of-plane deformation sequence of the five membered ring yields a simple quadratic-quartic potential function with a positive quadratic coefficient suggesting a planar structure for the molecule.

Poly(rA) • Poly(rU) with Ni2+ Ions at Different Temperatures: Infrared Absorption and Vibrational Circular Dichroism Spectroscopy

Abstract Phase transitions were studied of the sodium salt of poly(rA) •poly(rU) induced by elevated temperature without Ni2+ and with Ni2+ in 0.07 M concentration in D2O (∼0.4 [Ni]/[P]). The temperature was varied from 20° C to 90° C. The double-stranded conformation of poly(rA)•poly(rU) was observed at room temperature (20° C—23° C) with and without Ni2+ ions. In the absence of Ni2+ ions, partial double- to triple-strand transition of poly(rA) •poly(rU) occurred at 58° C, whereas only single-stranded molecules existed at 70° C. While poly(rU) did not display significant helical structure, poly(rA) still maintained some helicity at this temperature. Ni2+ ions significantly stabilized the triple-helical structure. The temperature range of the stable triple-helix was between 45° C and 70° C with maximum stability around 53° C. Triple-to single-stranded transition of poly(rA) •poly(rU) occurred around 72° C with loss of base stacking in single-stranded molecules. Stacked or aggregated structures of poly(rA) formed around 86° C. Hysteresis took place in the presence of Ni2+ during the reverse transition from the triple-stranded to the double-stranded form upon cooling. Reverse Hoogsteen type of hydrogen-bonding of the third strand in the triplex was suggested to be the most probable model for the triple-helical structure. VCD spectroscopy demonstrated significant advantages over infrared absorption or the related electronic CD spectroscopy.

Complexes of (dG-dC)20 with Mn2+ ions: a study by vibrational circular dichroism and infrared absorption spectroscopy.

The B-Z transition of the synthetic oligonucleotide, (dG-dC)20, induced by Mn2+ ions at room temperature, was investigated by absorption and Vibrational Circular Dichroism (VCD) spectroscopy in the range of 1800-800 cm(-1). Metal ion concentration was varied from 0 to 0.73 M Mn2+ (0 to 8.5 moles of Mn2+ per mole of oligonucleotide phosphate, [Mn]/[P]). While both types of spectra showed considerable changes as the Mn2+ concentrations were raised, differences between the two were often complementary in their expression and extent, those displayed by VCD being more clearly evident due to the inversion of the opposite helical sense from the right-handed to the left-handed conformation. The main phase of the transition occurred in the metal ion concentration between 0.8-1.1 [Mn]/[P]. Gradual changes that took place in the spectra were interpreted in terms of simultaneous processes that depended on metal ion concentration, namely B-Z transformation, binding of Mn2+ to phosphates and to nitrogen bases, and partial denaturation. Below approximately 0.6 [Mn]/[P], only a small portion of the oligonucleotide adopted the Z conformation within a 3 hour period, whereas conversion was completed in the same time interval for concentrations between 0.9-1.2 [Mn]/[P]. At [Mn]/[P] >1.7, complete transition to the Z-form took place immediately on adding Mn2+. Applying VCD spectroscopy in combination with conventional infrared absorption proved most useful for corroborating changes in the absorption spectra, and for detecting in an unique manner, not attainable by absorption methods, conformational changes that lead to the inversion of the helical sense of the oligonucleotide.

The ring puckering vibration of trimethylene sulfoxide: Far-infrared spectrum from 50 to 675 cm−1

Abstract A number of absorptions between 100 and 300 cm −1 in the infrared spectrum of trimethylene sulfoxide vapor have been observed and assigned to Δ v p = 1 and 2 transitions in the ring puckering mode. With the aid of a computer program providing for a potential function essentially of the form V ( x ) = V 2 x 2 + V 3 x 3 + V 4 x 4 ( x the dimensioned puckering coordinate), the barrier to inversion between the stable equatorial and a possible axial conformer is established to be 1205 cm −1 with an uncertainty of ±11 cm −1 at the worst or ±1 cm −1 at best, depending upon the assignment of several very weak absorptions. The axial well depth, depending more critically upon these assignments, is no greater than 150 cm −1 and may be as low as 5 cm −1 .

The ring-puckering vibration of methyl-substituted oxetans and thietans: far-infrared spectra from 50 to 500 cm−1

Abstract The vapour-phase infrared spectra in the range 50–500 cm −1 are reported for 2- and 3-methyl oxetan (2- and 3-MO), 2-methyl thietan (2-MT), 2,2-dimethyl oxetan (2,2-DMO) and 3,3-dimethyl thietan (3,3-DMT). The absorptions are interpreted as methyl deformation fundamentals and transitions within the ring-puckering manifold. Particular emphasis is placed on the latter, for which band sequences are analyzed with a general puckering potential function, V ( q ) = V ′ 2 q 2 + V ′ 3 q 3 + V ′ 4 q 4 , q being the dimensionless puckering normal coordinate. For the gem -dimethyl compounds for which V ′ 3 = 0, the barrier to ring inversion increases upon methyl substitution to 51.1 cm −1 for 2,2-DMO and 300.0 cm −1 for 3,3-DMT as compared to the parent molecules. The monomethyl compounds exist as stable equatorial and axial conformers at room temperature, the energy differences being 38.1, 43.8 and 117.6 cm −1 , and the inversion barriers 107.5, 98.7 and 341.1 cm −1 , respectively, for 2-MO, 3-MO and 2-MT. The trends in the potential function constants are discussed.

The out-of-plane ring deformations of 1,3- and 1,4-dioxene and 3,6-dihydro-2h-pyran: comparison of a series of cyclohexenes

Abstract The far-IR spectra (100–600 cm − ) of 1,3-dioxene and 3,6-dihydro-2H-pyran in the vapour phase are analyzed for the out-of-plane ring deformations. The fundamentals and a number of combination sequences are assigned. The spectrum of 1,4-dioxene is reexamined. The positions of these deformations in the three compounds are compared with those of cyclohexene and 2,3-dihydropyran. The twisting transitions are analyzed with a one-dimensional quadratic-quartic potential function. The barrier heights so derived, thought to represent approximate values for the barrier to planarity, decrease in the order 1,4-dioxene > 2,3-dihydropyran > 3,6-dihydro-2H-pyran > 1,3-dioxene.

The excitation scheme: A new method for calculation of vibrational circular dichroism spectra

An alternate procedure for calculating vibrational circular dichroism is proposed. The method eliminates the need to solve the magnetically perturbed SCF equations which leads to an overall decrease in computer time. Instead, an expansion over electronic excited states is partially used to estimate the molecular response to the magnetic field and nuclear displacements. A rigid orbital approximation is used for the electronic states. The rotational strengths obtained in this manner are compared to original experimental data for camphor and α-pinene, and previous calculations on propylene oxide and oxirane. In all cases good agreement of simulated spectral intensities with experiment is observed. Although extensive approximations had to be adopted in the current implementation, the excitation scheme yields results superior to those obtained by the classical MFP or VCT formulations of VCD for camphor and α-pinene, whereas MFP/GIAO theory performs better in the case of oxirane.

The vibrational spectra (100–1600 cm−1) and scaled abinitio STO‐3G and 3‐21G harmonic force fields for norbornane, norbornene, and norbornadiene

The vibrational spectra in the region of 100–1600 cm−1 of norbornane and norbornadiene are reinvestigated, and those of norbornene reported for the first time. On the basis of 3‐21G ab initio force fields, evaluated for each molecule and scaled using overlay refinements of 12 scaling factors, the spectra are assigned and the observed transition frequencies reproduced with an overall average error of 6.2 cm−1. STO‐3G force constants, modified to correct for deficiencies in the stretch/bend interaction force constants but otherwise scaled analogously to 3‐21G, reproduce the final set of assignments to within 10.1 cm−1 on average. The STO‐3G basis is shown to be suitable as a less costly alternative to split‐valence basis sets, particularly for describing the vibrational dynamics of low frequency ring bending and torsional modes.