Gauche Isomers Research Articles

A Theoretical View on the Conformer Stabilization of Butane

The rotational barrier and conformer energies of butane are well-known, but the contributing effects to its conformational isomerism are still unclear. Calculated potential energy surfaces for the relaxed and vertical (bond distances and angles frozen) structures, together with NBO analysis, suggest that approaching or distancing methyl groups involve substantial energy costs between the gauche and anti isomers, while hyperconjugative interactions play an important, but not prevalent, role for the conformational isomerism of butane.

Structurally Selective Geminate Rebinding Dynamics of Solvent-Caged Radicals Studied with Nonequilibrium Infrared Echo Spectroscopy

Cyclopentadienylmolybdenum(II) tricarbonyl dimer exists in two different equilibrium conformations: trans and gauche. Ultrafast photoexcitation in the ultraviolet cleaves the Mo-Mo bond, permitting observation of the subsequent geminate rebinding reaction (t(rebinding) = 31.6 ps) by monitoring infrared bleach recoveries at frequencies corresponding to the CO stretches of the trans and gauche isomers, the time-resolved measurements revealed that the monomers rebind in the trans configuration only. Further insight into the rebinding reaction was obtained by mapping the full potential energy surface along the reaction coordinate using electronic-structure methods.

Ether-like Si–Ge hydrides for applications in synthesis of nanostructured semiconductors and dielectrics

Hydrolysis reactions of silyl-germyl triflates are used to produce ether-like Si-Ge hydride compounds including H(3)SiOSiH(3) and the previously unknown O(SiH(2)GeH(3))(2). The structural, energetic and vibrational properties of the latter were investigated by experimental and quantum chemical simulation methods. A combined Raman, infrared and theoretical analysis indicated that the compound consists of an equal mixture of linear and gauche isomers in analogy to the butane-like H(3)GeSiH(2)SiH(2)GeH(3) with an exceedingly small torsional barrier of approximately 0.2 kcal mol(-1). This is also corroborated by thermochemistry simulations which indicate that the energy difference between the isomers is less than 1 kcal mol(-1). Proof-of-principle depositions of O(SiH(2)GeH(3))(2) at 500 degrees C on Si(100) yielded nearly stoichiometric Si(2)Ge(2)O materials, closely reflecting the composition of the molecular core. A complete characterization of the film by RBS, XTEM, Raman and IR ellipsometry revealed the presence of Si(0.30)Ge(0.70) quantum dots embedded within an amorphous matrix of Si-Ge-O suboxide, as required for the fabrication of high performance nonvolatile memory devices. The use of readily available starting materials coupled with facile purification and high yields also makes the above molecular approach an attractive synthesis route to H(3)SiOSiH(3) with industrial applications in the formation of Si-O-N high-k gate materials in high-mobility SiGe based transistors.

Redox State of Coenzyme Q10 Determines Its Membrane Localization

The interaction between oxidized (ubiquinone-10) and reduced (ubiquinol-10) coenzyme Q 10 with dimyristoylphosphatidylcholine has been examined by differential scanning microcalorimetry, X-ray diffraction, infrared spectroscopy, and (2)H NMR. Microcalorimetry experiments showed that ubiquinol-10 perturbed considerably more the phase transition of the phospholipids than ubiquinone-10, both forms giving rise to a shoulder of the main transition peak at lower temperatures. Small angle X-ray diffraction showed an increase in d-spacing suggesting a thicker membrane in the presence of both ubiquinone-10 and ubiquinol-10, below the phase transition and a remarkable broadening of the peaks indicating a loss of the repetitive pattern of the lipid multilamellar vesicles. Infrared spectroscopy showed an increase in wavenumbers of the maximum of the CH 2 stretching vibration at temperatures below the phase transition, in the presence of ubiquinol-10, indicating an increase in the proportion of gauche isomers in the gel phase, whereas this effect was smaller for ubiquinone-10. A very small effect was observed at temperatures above the phase transition. (2)H NMR spectroscopy of perdeuterated DMPC showed only modest changes in the spectra of the phospholipids occasioned by the presence of coenzyme Q 10. These small changes were reflected, in the presence of ubiquinol-10, by a decrease in resolution indicating that the interaction between coenzyme Q and phospholipids changed the motion of the lipids. The change was also visible in the first spectral moment (M1), which is related with membrane order, which was slightly decreased at temperatures below the phase transition especially with ubiquinol-10. A slight decrease in M 1 values was also observed above the phase transition but only for ubiquinol-10. These results can be interpreted to indicate that most ubiquinone-10 molecules are localized in the center of the bilayer, but a considerable proportion of ubiquinol-10 molecules may span the bilayer interacting more extensively with the phospholipid acyl chains.

Ionization Spectroscopy of Conformational Isomers of Propanal: The Origin of the Conformational Preference

Two different conformational isomers of propanal, cis and gauche, are investigated by the vacuum-UV mass-analyzed threshold ionization (VUV-MATI) spectroscopy to give accurate adiabatic ionization potentials of 9.9997 +/- 0.0006 eV and 9.9516 +/- 0.0006 eV, respectively. cis-Propanal, which is the more stable conformer in the neutral state, becomes less stable in the cation compared to gauche-propanal. Vibrational structures revealed in the MATI spectra indicate that cis and gauche isomers undergo their unique structural changes upon ionization. The ionization of gauche-propanal induces a geometrical change along the conformational coordinate, suggesting that the steric effect in the ground state is diminished upon ionization. Natural bonding orbital (NBO) calculations provide the extent of hyperconjugation in each conformational isomer of propanal.

Polarization Modulation Infrared Reflection Absorption Spectroscopy Investigations of Thin Silica Films Deposited on Gold. 2. Structural Analysis of a 1,2-Dimyristoyl-sn-glycero-3-phosphocholine Bilayer

In this paper we report on the structural analysis of bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) using polarization modulation infrared reflection absorption spectroscopy (PM IRRAS). The lipid bilayers were formed on SiO2|Au and Au surfaces using the Langmuir-Blodgett and Langmuir-Schaeffer techniques. As we showed in part 1 (Zawisza, I.; Wittstock, G.; Boukherroub, R.; Szunertis, S. Langmuir 2007, 23, 9303-9309), SiO2 layers of 7 nm thickness, synthesized by plasma-enhanced chemical vapor deposition on 200 nm thick gold covered glass slides, allow PM IRRAS investigations. Only minor changes in the order and structure of the lipid bilayer are observed when deposited on SiO2|Au and Au surfaces. The choline moiety in the leaflet directed toward the SiO2 surface exists in trans conformation and shows a tilt of 28 degrees with the surface normal of the CN bond. On the silica surface in the second leaflet directed toward air and in two layers deposited on the Au surface, trans and gauche isomers of the choline moiety are present and the tilt of the CN bond increases to 55 degrees with respect to the surface normal. The order and molecular orientation in the DMPC bilayers on SiO2 and Au surfaces are not affected by time. The analysis of the phosphate stretching mode on the Au surface shows slight dehydration of this group and reorientation of the phosphate moiety.

Calculations of vibrational frequencies, Raman activities and degrees of depolarization for complexes involving water, methanol and ethanol

Raman activities and degrees of depolarization are reported for 14 complexes involving methanol, ethanol and water using the MP2/aug-cc-pVDZ model. For ethanol both trans and gauche isomers are considered. The red-shifts of the OH stretching and the blue shifts of the bending τ CO–OH mode were analyzed for the proton-donor molecules upon hydrogen bond. The shift of the ν CO stretching mode of the alcohol molecules are also analyzed and found to be specific giving characterization of the amphoteric relation, being positive for the proton-acceptor and negative for the proton-donor molecule.

Conformation Equilibrium of 1,2-Dichloroethane as a Probe for Solvent Properties of Liquid and Supercritical CO2

Abstract Gibbs-energy difference between the gauche and trans isomers of 1,2-dichloroethane (DCE) in liquid and supercritical (SC) CO2 was investigated using Raman spectroscopy. The gauche isomer was relatively stabilized in these solvents compared with in non-polar organic solvents. This was attributed to the interaction of the dipolar gauche isomer with the quadrupole moment of the CO2 molecule, as well as the local density enhancement in SC CO2. Conformation equilibrium of DCE was suggested to be useful as a probe for studying solvent properties of SC fluids.

A computational study of dihalogen-μ-dichalcogenides: XAAX (X = F, Cl, Br; A = S, Se)

The structures of the dihalogen-μ-dichalcogenides FSSF, ClSSCl, BrSSBr, FSeSeF, ClSeSeCl, and BrSeSeBr have been studied using both density functional theory and coupled cluster theory. Other isomers with the empirical formula A 2X 2 are presented briefly, and it is demonstrated that the XAAX (gauche) isomer is the lowest energy structural form. Four families of correlation consistent basis sets of double- through quadruple-ζ quality were used, including the standard, augmented, tight d (core polarization), and augmented tight d sets. Fully optimized structures and vibrational frequencies, including anharmonic computations, are reported and compared with available experimental results. In the fluorine compounds, the A–A bond is shown to be shorter than its corresponding A 2 specie, which also occurs for the FOOF molecule [R.H. Jackson, J. Chem. Soc., (1962) 4585]. As well, increasing the halogen size increases the length of the A–A bond. This investigation demonstrates that this unique geometry is a consequence of anomeric delocalization of a chalcogen lone pair into an adjacent σ∗ orbital.

Structural Relaxation in Amorphous 1,2-Dichloroethane Studied by Transformation between Conformation Isomers

Structural relaxation in amorphous 1,2-dichloroethane (DCE) samples prepared by vapor deposition on cold substrates were studied by Raman scattering. The gauche and trans molecules of DCE were found to coexist in amorphous states immediately after the deposition, and structural relaxation occurred with temperature elevation before crystallization. Mole fraction of the gauche isomer increased during this relaxation process, although trans is the stable isomer in gaseous and crystalline states. At the final amorphous stage immediately before crystallization, the gauche mole fraction was close to the mole fraction of the supercooled liquid state. It was also found that trans molecules located at positions with lower density were more easily transformed into the gauche conformation, while the distribution of the local structure around the resultant gauche molecules remained almost unchanged during the structural relaxation. Such behaviors of amorphous DCE are discussed from the viewpoint of the characteristic molecular structure of DCE.

Synthesis, Structure and Spectral Properties of [Ni(TAMEN)](ClO4)2·DMF (TAMEN = N,N′‐Tetra(4‐antipyryl‐methyl)‐1,2‐diaminoethane), a Mannich Base Complex of Biological Relevance

AbstractThe new mononuclear complex [Ni(TAMEN)](ClO4)2·DMF (TAMEN = N,N′‐tetra‐(4‐antipyrylmethyl)‐1,2‐diaminoethane) has been synthesized and its crystal structure was determined by single‐crystal X‐ray diffraction. It crystallizes with monoclinic symmetry, space group P21/c (no. 14) and unit cell parameters of a = 10.8736(3), b = 10.9560(4), c = 45.820(2) Å, β = 90.23(1)°, Z = 4. The TAMEN molecule acts as a hexadentate ligand incorporating a 1,2‐diaminoethane bridge in the staggered conformational gauche isomer. The nickel(II) ion is octahedrally coordinated with metal‐ligand distances ranging from 2.023(2) to 2.145(3) Å. Electronic and vibrational spectroscopy data agree well with the crystal structure.

Efficient Synthesis of the Os−Os Dimers [Cp(CO)2Os]2, [Cp*(CO)2Os]2, and [(iPr4C5H)(CO)2Os]2 and Computational Studies on the Relative Stabilities of Their Geometrical Isomers

The Os−Os dimer [Cp(CO)2Os]2 was synthesized in good yield by reaction of Cp(CO)2OsI with NaK. The related Cp* dimer [Cp*(CO)2Os]2 (Cp* = η5-C5Me5) was prepared by reaction of Cp*(CO)2OsH with 2,2‘-azobis(isobutyrylnitrile) (AIBN). In contrast to [Cp(CO)2Os]2, which has only terminal CO ligands, spectroscopic and crystallographic data indicate that [Cp*(CO)2Os]2 has two bridging CO ligands. Reaction of tetraisopropylcyclopentadiene with [(CO)3OsI]2 provides (iPr4C5H)(CO)2OsI, which can be converted to (iPr4C5H)(CO)2OsH through reduction with NaK followed by treatment with EtOH. Reaction of (iPr4C5H)(CO)2OsH with AIBN gives [(iPr4C5H)(CO)2Os]2, which is much more soluble than [Cp*(CO)2Os]2. DFT (B3LYP) calculations on these Os−Os dimers reveal the energetics of different geometrical isomers. The anti and gauche isomers of [Cp(CO)2Os]2, with terminal CO ligands, are significantly more stable than the trans and cis isomers with bridging CO ligands, while the stability of the anti isomer of [Cp*(CO)2Os]2 is s...

Conformational equilibria in liquids consisting of small chain molecules

The conformational equilibrium in neat liquids consisting of small chain molecules, n-butane and 1,2-dichloroethane, is studied by means of a RISM-type integral equation theory formulated by Yoshida and co-workers [T. Munakata, S. Yoshida, F. Hirata, Phys. Rev. E 54 (1996) 3687]. Conformational shift toward the gauche isomer was observed upon transferring from gas to liquid phases in the both fluids in harmony with experiments. The equilibrium constant for 1,2-dichloroethane shows very small temperature dependence. The pressure dependence of the equilibrium constant indicates that the gauche isomer is in favor at higher temperature. The theoretical results are consistent with the experimental observations.

Infrared spectra and conformational analysis of anti and gauche deuterated ethanol isotopomers

The infrared spectra of dilute CCl 4 solutions of deuterated ethanol isotopomers have been examined in the fundamental OH/OD stretching absorption regions. The compounds studied are comprised of undeuterated CH 3CH 2OH, and four deuterated isomers, CH 3CD 2OH, CD 3CH 2OH, CH 3CH 2OD, and CD 3CD 2OD. Doublet character of the high energy IR hydroxy band, indicating the existence of anti and gauche conformational isomers, is found for each isotopomer in agreement with previous IR studies of primary saturated alkanols. A variable temperature study of the deconvoluted spectra for the undeuterated ethanol system provides a reference experimental estimate of the relative enthalpies of the C s (anti) and C 1 (gauche) conformers. The analysis also allows a determination of the intensities of the individual bands. Spectral and thermodynamic results from HF/6-311++G* calculations are compared with the experimental observations. The deconvoluted spectra for the deuterated isomers are compared to the ethanol results, and small differences in OH absorption band frequencies are observed. The equilibrium constants for gauche to anti conversion for two OD compounds are somewhat larger than those for the three OH isomers.

Thermal analysis and Raman spectroscopic studies of crystallization in poly(ethylene 2,6-naphthalate)

The combination of Fourier transform Raman spectroscopy and thermal analysis has been proved to be adequate for the study of the quantitative structural changes which take place in amorphous poly(ethylene 2,6-naphthalate) on annealing. Different conformer contents were found in the annealed samples depending on annealing conditions. In general, annealing of the amorphous poly(ethylene 2,6-naphthalate) from the glassy state induces a conformational transition of gauche to trans. The structure obtained during crystallization is characterized by a three-phase conformational model, including an amorphous phase, a rigid amorphous phase and a crystalline phase. The crystallization is further characterized by a three-zone process, firstly a primary crystallization process, secondly a variation of the rigid amorphous phase with a constant value of the crystalline phase and thirdly a secondary crystallization process. The bandwidth at half intensity at 1721cm−1 in the Raman spectrum varied between 32cm−1 for the complete amorphous phase and 7cm−1 for the total rigid phase, the sum of the rigid amorphous and crystalline phase. The bandwidth at half intensity at 1721cm−1 was directly related to the amount of the total rigid phase and confirmed by the variation of the heat capacity increase at the glass transition temperature. Two complementary bands in the Raman spectrum, at 1107 and 1098cm−1, were found to be related to the trans and gauche isomers. A difference was measured between the total trans content and the amount of rigid phase due to the presence of some trans conformations in the amorphous phase. The extrapolation of the bandwidth at half intensity at 1721cm−1 to the value of zero, corresponding to the complete crystalline phase, gave a melting enthalpy of 196J/g and the corresponding density of the crystalline phase was 1.4390g/cm3. A complete rigid phase structure was obtained by a melting enthalpy of 144J/g and a density of 1.4070g/cm3.

The torsional problem of oxalyl chloride: a challenge for theoretical methods

The internal rotation of oxalyl chloride is investigated through ab initio Hartree–Fock and density functional theory methods. The most stable conformation is planar trans and a quasi-stable gauche isomer appearing about midway between the trans and cis isomers was also detected by the two methods. Stabilization of trans isomer is not only due to strong overlaps but also to through space interactions whereas the gauche conformation appears to be mainly stabilized by through bond interactions. In addition, the energy barrier at the cis conformation has been found to be mainly due to through space interactions.

Correlation between the effect of the anti-neoplastic ether lipid 1-O-octadecyl-2-O-methyl-glycero-3-phosphocholine on the membrane and the activity of protein kinase Calpha.

The antineoplastic ether phospholipid 1-O-octadecyl-2-O-methyl-sn-glycero-3-phophocholine (ET-18-OCH3) was incorporated into dimyristoylglycerophosphocholine (Myr2Gro-PCho)/dimyristoylglycerophosphoserine (Myr2Gro-PSer) (4 : 1 molar ratio) mixtures. Electron microscopy showed that the addition of ET-18-OCH3 reduced the size of the vesicles. Small vesicles could be detected even at 60 mol% ET-18-OCH3. Sedimentation studies showed the increasing presence of phospholipids in the supernatant, while turbidity measurements indicated a decrease in absorbance as the ET-18-OCH3 concentration was increased. These findings may be explained by the formation of small vesicles and/or mixed micelles. Infrared spectroscopy showed that at 60 mol% the fluidity of the membrane was considerably increased at temperatures below the phase transition, with only a small increase in the proportion of gauche isomers after the gel-to-fluid phase transition of this sample. On the other hand, protein kinase Calpha (PKCalpha) activity progressively decreased when ET-18-OCH3 was incorporated into multilamellar vesicles, reaching a minimum value at 20 mol%, this inhibition being attributed to the modification of the membrane produced by a cone-shaped molecule. At higher concentrations, however, ET-18-OCH3 activated the enzyme with a maximum being attained at 50 mol%. This activation being attributed to the formation of small vesicles and/or micelles. At still higher concentrations of ET-18-OCH3 the enzyme was once again inhibited, inhibition being almost complete at 80 mol%. When PKC was assayed using large unilamellar vesicles a slight activation was observed at very low ET-18-OCH3 concentrations.

Thermal Chemistry of C3 Allyl Groups on Pt(111)

The thermal chemistry of allyl iodide and of allyl bromide adsorbed on Pt(111) was investigated by temperature-programmed desorption (TPD) and reflection−absorption infrared (RAIRS) spectroscopies. On the clean Pt(111) surface, both allyls were found to bond to the surface via the halogen atom in a gauche conformation and with the C−C−C plane close to parallel to the surface. In the presence of surface hydrogen, allyl iodide was found to tilt backward such that the C−C−C plane adopts a more vertical orientation on the surface; in this more upright geometry, both cis and gauche isomers were identified. With both molecules the facile thermally activated cleavage of the carbon−halogen bond results in the formation of C3 allylic species on the surface. A η1 allylic moiety was identified by RAIRS in the high-exposure regime of allyl iodide after annealing to 200 K, and the formation of a second η3 allylic intermediate was inferred from TPD experiments with coadsorbed hydrogen and deuterium. At low surface conc...

Real-time FTIR and WAXS studies of drawing behavior of poly(ethylene terephthalate) films

The development of molecular orientation and crystallization was studied during uniaxial drawing of poly(ethylene terephthalate) (PET) films, which was immediately followed by subsequent taut annealing at the drawing temperature. The behavior was monitored in real time throughout the drawing and annealing using dynamic FTIR spectroscopy and in situ WAXS measurements using the Daresbury Synchrotron Radiation Source. Films were drawn at 80 and 85°C at varying strain rates (0.001–0.7 s−1). The true stress–strain behavior was determined at each of the drawing conditions and the density and optical anisotropy of unloaded samples was measured. The IR spectra were analyzed using curve reconstruction procedures developed previously, and they showed that orientation of the phenylene groups and the trans glycol conformers occurred before significant gauche–trans conformational changes could be seen. The onset of crystallization, defined as the point that the crystalline 105 reflection could be first observed using WAXS, was not found to correlate with any specific change in the proportions of trans and gauche isomers nor with any feature on the stress–strain curve. However, it was clear that, for these comparatively low strain rates, crystallization occurred during the drawing process while the crosshead was moving and the draw ratio was increasing. The orientation of the crystallites was calculated from the 105 reflection observed in a tilted film, transmission geometry. The crystallites were found to form at a draw ratio of about 2.5 with high orientation values (P2> 0.8) that increased during drawing and annealing to P2 values of 0.95, irrespective of the drawing conditions. Semiquantitative measurements of crystallinity showed that the fraction of crystalline material that developed during drawing decreased with increasing strain rate. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 1825–1837, 2001

Direct Evidence for a Lipid Alkyl Chain Ordering Transition in Poly(ethylene oxide) Lipopolymer Monolayers at the Air−Water Interface Obtained from Infrared Reflection Absorption Spectroscopy

Lipopolymers are lipids with a polymer chain covalently attached to the lipid. At the air−water interface such lipopolymers may undergo up to two monolayer phase transitions. One is correlated with desorption of the polymer group from the surface (the so-called pancake−mushroom transition) and a second is “native” to lipopolymers in the sense that it can only be observed when lipid and polymer are present in the same molecule. In this study we present direct evidence from infrared spectroscopy showing that the “native” transition, although requiring the presence of the polymeric headgroup, is a transition solely within the lipid alkyl chains. This transition correlates to a strong reduction of the number of gauche isomers within the lipid alkyl chains. We used two poly(ethylene oxide) lipopolymers which differed only in the lipid alkyl chains. These were either fully deuterated or fully protonated. The polymer chains were protonated in both cases. Within the protonated lipopolymer, a strong ordering of th...