Structures,vibrational spectra,and relative energetics of FC(O)ONO and FC(O)NO2 isomers at DFT and ab initio levels

The structural and vibrational parameters of FC(O)ONO and FC(O)NO₂ isomers were examined theoretically using the B3LYP/6-311+G(3df) and CCSD(T)/6-311G(d) methods. Four conformers of FC(O)ONO isomer and one FC(O)NO₂ isomer are found here. Among them, the trans–cis and cis–cis FC(O)ONO configuration are new conformers. The energetics were refined with G3//B3LYP and CBS-QB3 calculations. The trans–trans conformer of the FC(O)ONO isomer is found to be the lowest energy structure, with an estimated heat of formation of ?104.9 kcal mol^?1 at 0 K as determined from CBS-QB3 theory. The next lowest structure is the cis–trans FC(O)ONO lying 1.7 kcal mol^?1 above the trans–trans structural form. The highest energy structure is the FC(O)NO₂ isomer with a predicted heat of formation of ?84.8 kcal mol^?1. A comparison of the relative stability of the FCNO₃ isomers with the isomers of ClCNO₃ shows that the Cl analogues follow the same pattern of stability, as do the F isomers. However, the chlorine isomers are unstable relative to their fluorine analogues.     

Enthalpies of formation and isomerization of cis‐ and trans‐decalin,and their oxa‐analogs by G3(MP2)//B3LYP calculations

G3(MP2)//B3LYP calculations have been carried out on trans‐ and cis‐decalin, and their mono‐, di‐, tri‐, and tetraoxa‐analogs. The main purpose of the work was to obtain enthalpies of formation for these compounds, and to study the relative stabilities of the cis–trans and positional isomers of the various (poly)oxadecalins. Comparison of the computational enthalpies of formation with the respective experimental ones, known only for the decalins and 1,3,5,7‐tetraoxadecalins, shows that in both cases the computational values are more negative than the experimental ones, the deviations being ?5 to ?7 kJ mol^?1 for the decalins and ?12 to ?17 kJ mol^?1 for the 1,3,5,7‐tetraoxadecalins. The respective computational enthalpies of cis–trans isomerization, however, are in excellent to satisfactory agreement with the experimental data. The cis–trans enthalpy differences vary from +11.0 kJ mol^?1 for decalin to ?15.4 kJ mol^?1 for 1,4,5,8‐tetraoxadecalin. Low relative enthalpy values were also calculated for the cis isomers of 1,8‐dioxadecalin (?3.7 kJ mol^?1), 1,3,6‐trioxadecalin (?4.6 kJ mol^?1), 1,3,8‐trioxadecalin (?9.7 kJ mol^?1), 1,4,5‐ trioxadecalin (?5.6 kJ mol^?1), 1,3,5,8‐tetraoxadecalin (?7.3 kJ mol^?1), and 1,3,6,8‐tetraoxadecalin (?14.5 kJ mol^?1). Copyright © 2009 John Wiley & Sons, Ltd.     

Investigations on the geometrical isomers of astaxanthin: Raman spectroscopy of conjugated polyene chain with electronic and mechanical confinement

Recent research interests in geometrical isomers of astaxanthin (AST) are motivated by their metabolic activities in aquatic animals and human. It has been established that cis‐isomers of AST are selectively absorbed in human plasma during the metabolic process; however, exact absorption mechanism is still unclear. Hence, a detailed investigation of the structural and optical properties of geometrical isomers of AST is required. Among the techniques available for the study of AST and other carotenoids, Raman spectroscopy has been much acclaimed. Raman spectra have been shown to be influenced by the electronic and mechanical confinement effects arising from the conjugated polyene chain of carotenoids. In this work, we present Raman studies of geometrical isomers of AST, along with their optical absorption characteristics. Geometrical isomers of AST were prepared by heating all trans‐AST in solution form, and the isomers were separated using high performance liquid chromatography. Optical absorption spectra of cis‐isomers of AST showed hypsochromic shifts in the main absorption band and formation of new bands at lower wavelengths. A detailed Raman spectral analysis performed on the cis‐isomers of AST showed new modes which have not been observed and accounted for so far. In addition, we demonstrate that the electronic and mechanical confinement effects in the polyene chain of AST play an important role in the Raman spectra of geometrical isomers of AST. It is anticipated that this work will demonstrate that Raman spectroscopy is an important diagnostic tool in distinguishing and identifying the geometrical isomers of AST. Copyright © 2014 John Wiley & Sons, Ltd.     

Micro‐Raman study of PET single fibres under high hydrostatic pressure: phase/conformation transition and amorphization

The micro/nano structural evolution of a PET single fibre under hydrostatic pressure has been studied by Raman micro spectroscopy in a diamond anvil cell (DAC). Different bands in the Raman spectra were used as probes: the low wavenumber collective modes (<250 cm⁻¹) representative of the long‐range chain organization, as well as the stretching and bending amide and aromatic ring modes representative of the local chain behaviour. The in situ analysis at different pressures shows an evolution from an axial oriented trans‐conformation to an amorphous, isotropic material, i.e. the reverse transformation observed during the process of drawing the fibre from an isotropic amorphous precursor. Copyright © 2007 John Wiley & Sons, Ltd.     

Raman spectroscopic characterization of a thiophene‐based active material for resistive organic nonvolatile memories

A combined theoretical and experimental Raman study is presented on a diphenyl bithiophene molecule known as a good candidate for the development of organic nonvolatile memory devices. Spectroscopic markers suitable to distinguish the different stable conformers of the molecule have been predicted and detected. The combined analysis of theoretical and experimental Raman spectra recorded in solution indicates that at room temperature a dynamical equilibrium, characterized by interconversion between the two more stable conformers (namely trans and cis), takes place and that the more populated species is the cis form. Referring to the solid phase instead, Raman spectra of single‐crystal samples show the presence of the only trans conformer, as confirmed by X‐ray measurements. Finally, Raman spectra of thin films, as those used for the memory device, were collected; samples just deposited from solution and after few hours from the deposition were analyzed. Following the evolution of selective spectroscopic Raman markers, an isomerization process from the abundant cis (as‐deposited) to the totally trans (after few hours) conformer in the solid phase was detected. These results open the way to the identification of the molecular isomers present in the thin film of the memory cell and finally of the active molecular species involved in the switching mechanism of the operating device. Copyright © 2009 John Wiley & Sons, Ltd.     

IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Evaluation of various DFT protocols for computing 1H and 13C chemical shifts to distinguish stereoisomers: diastereomeric 2‐, 3‐, and 4‐methylcyclohexanols as a test set

¹H and ¹³C NMR chemical shifts were measured for a set of six isomers—the cis and trans 2‐, 3‐, and 4‐methylcyclohexanols. ¹H and ¹³C NMR chemical shifts were computed at the B3LYP, WP04, WC04, and PBE1 density functional levels for the same compounds, taking into account the Boltzmann distribution among conformational isomers (chair–chair forms and hydroxyl rotamers). The experimental versus computed chemical shift values for proton and carbon were compared and evaluated (using linear correlation (r²), total absolute error (|Δδ|_T), and mean unsigned error (MUE) criteria) with respect to the relative ability of each method to distinguish between cis and trans stereoisomers for each of the three constitutional isomers. For ¹³C shift data, results from the B3LYP and PBE1 density functionals were not sufficiently accurate to distinguish all three pairs of stereoisomers, while results using the WC04 functional did do so. For ¹H shift data, each of the WP04, B3LYP, and PBE1 methods was sufficiently accurate to make the proper stereochemical distinction for each of the three pairs. Applying a linear correction to the computed data improved both the absolute accuracy and the degree of discrimination for most of the methods. The nature of the cavity definition used for continuum solvation had little effect. Overall, use of proton chemical shift data was more discriminating than use of carbon data. Copyright © 2007 John Wiley & Sons, Ltd.     

SERS as a probe for adsorbate orientation on silver nanoclusters

Surface‐enhanced Raman scattering (SERS) spectroscopy has been used to characterize multilayers of three isomeric aromatic compounds adsorbed on silver nanoclusters. The three structural isomers, all of which adsorb in the carboxylate form onto the silver nanoclusters, bind in two different geometries to the silver surface. Different molecular configurations correlate to differences in bonding strength of these molecules to the silver surface, which can be probed by SERS. For ortho‐hydroxybenzoic acid (salicylic acid), we observed red shifts of major SERS peaks in comparison to the normal Raman vibrations of nonadsorbed crystalline material. For this molecule the steric hindrance between the adjacent carboxylate and hydroxyl groups causes the carboxylate group to rotate from the common flat geometry of benzene substituents on surfaces and bond directly through one of the oxygen atoms to the surface. In this case, strong coordinative bonding between the carboxylate group and the metal surface causes the red shifts in the SERS peaks. For para‐, and meta‐hydroxybenzoic acid, the steric hindrance is less likely since the two functional groups are not at adjacent positions, and therefore these molecules adsorb on the silver surface in a totally flat geometry. For these molecules, in contrast to the ortho isomer, the CO₂ interacts with the surface through an extended π bond, and these molecules are physically adsorbed in the common flat position. Therefore, for the meta and para substituents, we do not observe significant red shifts in the SERS spectrum. Copyright © 2009 John Wiley & Sons, Ltd.     

A reevaluation of the assignment of the vibrational fundamentals and the rotational analysis of bands in the high-resolution infrared spectra of trans- and cis-1,3,5-hexatriene

Assignments of the vibrational fundamentals of cis- and trans-1,3,5-hexatriene are reevaluated with new infrared and Raman spectra and with quantum chemical predictions of intensities and anharmonic frequencies. The rotational structure is analyzed in the high-resolution (0.0013-0.0018 cm⁻¹) infrared spectra of three C-type bands of the trans isomer and two C-type bands of the cis isomer. The bands for the trans isomer are at 1010.96 cm⁻¹ (ν₁₄), 900.908 cm⁻¹ (ν₁₆), and 683.46 cm⁻¹ (ν₁₇). Ground state (GS) rotational constants have been fitted to the combined ground state combination differences (GSCDs) for the three bands of the trans isomer. The bands for the cis isomer are at 907.70 cm⁻¹ (ν₃₃) and 587.89 cm⁻¹ (ν₃₅). GS rotational constants have been fitted to the combined GSCDs for the two bands of the cis isomer and compared with those obtained from microwave spectroscopy. Small inertial defects in the GSs confirm that both molecules are planar. Upper state rotational constants were fitted for all five bands.     

UV filter 2‐ethylhexyl 4‐methoxycinnamate: a structure,energetic and UV–vis spectral analysis based on density functional theory

2‐Ethylhexyl 4‐methoxycinnamate (EHMC) is a very commonly used UVB filter that is known to isomerize from the (E) to the (Z) isomer in the presence of light. In this study, we have performed high level quantum chemical calculations using density functional theory (DFT) with the B3LYP density functional and extended basis sets to study the gas‐phase molecular structure of EHMC and its energetic stability. Calculations were also performed for related smaller molecules cinnamic acid and 4‐methoxycinnamic acid. Charge delocalization has been analyzed using natural charges and Wiberg bond indexes within the natural bond orbital analysis and using nucleus independent chemical shifts. Density functional theory calculations reveal that the (E) isomer of EHMC is more stable than the (Z) by about 20 kJ mol^?1 in both the gas and aqueous phases. The enthalpy of formation in the gas phase of (E)‐EHMC was derived from an isodesmic bond separation reaction. Long‐range corrected DFT calculations in implicit water were made in order to understand the excited state properties of the (E) and (Z) isomers of EHMC. Copyright © 2013 John Wiley & Sons, Ltd.     

Stark spectroscopy with the CO laser: The ν2 fundamental bands of trans- and cis-nitrous acid,HNO2, in the 6-μm region

The ν₂ fundamental bands of trans- and cis-HNO₂ have been studied by the technique of intracavity CO laser Stark spectroscopy. Excited-state rotational constants were determined, and the ν₂-band origins were found to be 1699.760 cm^?1 for the trans isomer and 1640.517 cm^?1 for the cis isomer. The total dipole moments for the ground and excited (v₂ = 1) vibrational states were found to be μ″ = 1.930 D and μ″ = 1.852 D for trans-HNO₂, and μ″ = 1.428 D and μ″ = 1.441 D for cis-HNO₂.     

High concentration trans form unsaturated lipids detected in a HeLa cell by Raman microspectroscopy

High concentration trans form unsaturated lipids have been found in a HeLa cell by Raman microspectroscopy. Two CC stretch bands are observed simultaneously at 1669 cm⁻¹ (trans form) and at 1656 cm⁻¹ (cis form) in a Raman spectrum obtained from a small area (1 µm in diameter) in a HeLa cell. The intensity ratio 1669/1656 indicates that the concentration of the trans form is as high as that of the cis. It is demonstrated that Raman microspectroscopy provides a powerful and unique means for in situ and noninvasive structural characterization of unsaturated lipids in a living cell. Copyright © 2008 John Wiley & Sons, Ltd.     

Formic acid in deuterium and hydrogen matrices

ABSTRACT

Formic acid (HCOOH, FA) was studied experimentally, by infrared spectroscopy, in H₂ and D₂ matrices, with focus on the preparation and characterisation in these matrix media of structures containing the higher-energy (cis) conformer. The cis-FA monomer and the cis-FA^?…?N₂ complex were successfully produced by selective vibrational excitation of corresponding trans-FA based species, and vibrationally characterised. The tunneling-induced conversion of the cis-FA^?…?N₂ complex in the studied matrices into the corresponding trans-FA complex was also investigated, and the found tunnelling properties discussed, in particular in comparison with those observed for the spontaneous conversion of cis-FA monomer into trans-FA. This article constitutes the first report on the infrared spectrum of FA conformers and stability of cis-FA monomer in a D₂ matrix, and on the structure, spectroscopy and stability of the cis-FA^?…?N₂ complex in both H₂ and D₂ matrices. Different attempts to prepare the cis-FA^?…?H₂O complex in the two investigated matrices are also described in detail, both from previously in situ generated cis-FA monomer followed by thermal mobilisation and by direct selective vibrational excitation of the trans-FA-H₂O complex.     

A Mössbauer effect study of the bonding in several organoiron carbonyl clusters

After a brief review of the applications of the Mössbauer effect to cyclopentadienyl containing compounds, the chemistry and spectral properties of the various iron carbonyl complexes are described. The electronic properties of a series of trinuclear and tetranuclear organoiron clusters have been investigated through Fenske-Hall self-consistent field molecular orbital calculations, and the results are compared with the Mössbauer effect isomer shifts. A linear correlation is found between the Slater effective nuclear charge, as calculated from the Fenske-Hall partial orbital occupancy factors, and the isomer shift. In these compounds the 4s orbital populations are rather constant. However, thecis andtrans isomers of [CpFe(CO)₂]₂ have a significantly lower 4s orbital populations. In this case, the reduced 4s population must be accounted for by adding it to the effective nuclear charge to obtain a good correlation with the isomer shift.     

Kinetic analysis of the photochemically and thermally induced isomerization of an azobenzene derivative on Au(111) probed by two-photon photoemission

Two-photon photoemission (2PPE) spectroscopy is employed to quantify the photochemically and thermally induced trans ⇌ cis isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on an Au(111) surface. The isomerization of TBA is accompanied by significant changes in the electronic structure, namely different energetic positions of the lowest unoccupied molecular orbital of both isomers and the appearance of an unoccupied final state for cis-TBA. A quantitative analysis of these effects allows the calculation of cross sections for the reversible isomerization and determination of the ratio between both isomers in the photostationary state, where 55±5% of the molecules are switched to cis-TBA. The cross section for the photoinduced trans → cis isomerization is 3.3±0.5×10⁻²² cm², while for the back reaction, a value of 2.7±0.5×10⁻²² cm² is obtained. Furthermore a pronounced reduction of the activation energy by a factor of four compared to the free molecule is found for the thermally activated cis → trans isomerization of the surface-adsorbed TBA. This demonstrates that the potential energy landscape of the adsorbed TBA is remarkably different from the liquid phase.     

Pyrolysis of amines: Infrared spectrum of 1-aminopropene

The infrared absorption spectrum of 1-aminopropene was observed for the first time in the gas phase. This molecule was produced by the thermal decomposition of cyclopropylamine. Two rotational isomers, cis and trans around the C=C double bond, occur. The relative yield of the conformers depends on the experimental conditions. The main conformer could not be identified experimentally, but an ab initio MO calculation suggests that the trans conformer is a little more stable form than the cis. These empirical assignments of the vibrational modes are supported by the ab initio MO calculation.     

Raman scattering study of the soft mode in Pb(Mg1/3Nb2/3)O3

Systematic Raman scattering experiments were performed on Pb(Mg_1/3Nb_2/3)O₃ (PMN) single crystals to resolve the low‐wavenumber dynamics in the crystal. Careful checking of the angular dependence of the Raman spectra indicated that the intense peak around 45 cm⁻¹, which always smears the low‐wavenumber spectra, stems from the F_2g mode due to Mg:Nb = 1:1 chemically ordered Fm3 m region. A proper scattering configuration for eliminating the strong F_2g mode allowed the observation of the lowest wavenumber soft mode dynamics in PMN. The results revealed the softening of the mode towards T_c with underdamped oscillation. The soft mode becomes overdamped in a wide temperature range above T_c, suggesting the development of cluster dynamics due to polar nanoregions. It recovers the underdamped oscillation and hardens in the high‐temperature region. Finally, the physical picture of the relaxor phenomenon in PMN is discussed in terms of lattice dynamics by comparison with the typical displacive‐type ferroelectric phase transition. Copyright © 2010 John Wiley & Sons, Ltd.