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.     

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.     

Possible spectroscopic manifestation of the angular group induced bond alteration (AGIBA) effect in toluene

The most obvious consequence of the concept of aromaticity is the common confidence that in aromatic compounds, bond lengths do not alternate and are between typical to the single and double ones. However, in 1994, performing crystal structure investigations of substituted pyridines and their salts, Krygowski and co‐workers have discovered a very surprising angular group induced bond alteration (AGIBA) effect: It appears that some angular substituents, like methoxy or nitrozo groups, can induce bond alternation in aromatic rings. Crystal studies do not allow one to operate with liquids that are more common in organic chemistry. This paper presents the first possible evidence of spectroscopic manifestations of the AGIBA effect. Raman spectra of the liquid toluene are analyzed. It is found that instead of being single, the line corresponding to the ring breathing vibrations is clearly split by 1.0–1.4 cm^?1, thus indicating the presence of two (cis‐ and trans‐) AGIBA isomers. The energy difference between these isomers estimated in temperature dependent Raman studies is found equal to 6.68 kJ mol^?1. The low‐wavenumber line therefore corresponds to the cis‐AGIBA isomer and the high‐wavenumber line to the trans‐AGIBA isomer stabilized by the AGIBA effect. 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.     

REMPI and IR-UV double resonance spectroscopy of 3-aminophenol·(NH3)1 cluster in the gas phase

The electronic and geometric structures of the cluster consisting of 3-aminophenol (3AP) and one ammonia molecule were investigated using resonance-enhanced multiphoton ionization and IR-UV double resonance spectroscopy in the gas phase. Between the cis and trans isomers found for the bare 3AP molecule, only trans isomer was found for 3AP·(NH₃)₁. It was found that complete quenching of the excited state of cis isomer, e.g. by conformer-specific excited state hydrogen transfer reaction, does not seem to occur, but that efficient conformational cooling drives the ground state population into the most stable trans isomer. The 0-0 band of the trans-3AP·(NH₃)₁ at 34 409 cm⁻¹ is red-shifted by 68 cm⁻¹ from that of the trans-3AP at 34 477 cm⁻¹. The IR depletion spectrum shows that the OH stretching vibration (3296 cm⁻¹) is red-shifted by 362 cm⁻¹ from that of the bare molecule. The large red-shift in OH frequency, combined with MP2 calculation, reveals that the structure of the cluster is the one with the nitrogen atom of ammonia bound to the hydroxyl hydrogen of aminophenol.     

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.     

Influence of hydrogen bonds and double bonds on the alkane and alkene derivatives self-assembled monolayers on HOPG surface: STM observation and computer simulation

The adsorption structure and hydrogen-bonded complexes of alkane and alkene derivatives self-assembled on HOPG were studied by scanning tunneling microscopy (STM) and Molecular Mechanics (MM) simulations. The effect of different interior -CHCH- conformations and functional groups in molecules on the structure and stability of self-assembled monolayers was considered. It was found that octadecanol and trans-oleic acid could form stable structure on HOPG and their high-resolution images could be obtained by STM. Octadecanol exhibited two kinds of packing by alkyl-alkyl and adsorbate-substrate interactions. The interior trans-CHCH- group in trans-oleic acid had a slight influence on the self-assembly configuration. However, owing to the cis-double bond in the interior of cis-oleyamine molecule, the ordered monolayer could not be easily imaged by STM at ambient conditions. The adsorption conformations of three kinds of molecules on HOPG surface were optimized by MM simulation, respectively. The analysis of hydrogen-bond interactions by computation stimulation also revealed that the stability of cis-oleyamine on HOPG was the worst. These results demonstrated that molecular self-assembly and its stability could be significantly tailored by changing the molecular structure.     

Substituent effects on the conformational stability of allyl fluorides

By the B3P86/6‐311G(3d,2p) method, remote substituent effects on trans‐YCH?CHCH₂F were investigated by examining their conformational stabilities, molecular geometries, and stereoelectronic interactions in this paper. The cis conformer is favored for Y?H, Cl, Me, Vinyl, CF₃, CN, CHO, and NO₂, whereas the gauche is favored for Y?OMe, OH. A correlation of ΔH with the substituent constants σ⁺(Y) shows that the increasing electron‐withdrawing ability of the substituent Y increases the relative stability of the cis conformer. It was found that the substituent effect on the molecule stabilization energies (relative to CH₂?CHCH₂F) is more significant in the gauche conformers than in the cis conformers. In agreement, molecular structures of the gauche conformers were also observed to vary more significantly with the substitution than those of the cis conformers. By the second‐order perturbation energy (E(2)) in NBO analysis, it was found that the total C₂–C₃ vicinal hyperconjugation is determinant in the enthalpy difference and consequently controls the conformational stability. Further analysis shows that the substituent effect on the C₂–C₃ vicinal hyperconjugations is much higher in the gauche conformers than in the cis conformers. The highly sensitive π_C?C→σ*_{C? F} interaction to the substitution in the gauche conformers, is the leading factor in variation of molecular stability and geometry. Copyright © 2010 John Wiley & Sons, Ltd.     

Vibrational analysis and conformational studies of allylamine

Infrared absorption spectra of allylamine and its amino-deuterated species were observed in the gas phase and in the low-temperature Ar matrix. An analysis of the spectra showed that there exist mainly three rotational conformers, and possibly one other conformer as a minor component. At room temperature, the skew forms around the CC bond populate about 70%, while the rest are assigned to the cis form(s). On the other hand, two forms around the CN bond, gauche and trans, exist with about equal populations.     

Vibrational spectroscopy of trans and cis deuterated formic acid (HCOOD): Anharmonic calculations and experiments in argon and neon matrices

The absorption spectra of trans and cis conformers of deuterated formic acid (HCOOD) isolated in argon and neon matrices are analyzed in the mid-infrared and near-infrared spectral regions (7900-450 cm⁻¹). Vibrational excitation by narrow-band IR radiation is used to convert the lower-energy trans conformer to the higher-energy cis form. A large number of overtone and combination bands are identified. The results of anharmonic vibrational calculations (CC-VSCF) for both conformers are reported and compared to the experimental spectra.     

Anharmonic force fields of cis- and trans-S1 C2H2

We calculate second-order vibrational perturbation theory (VPT2) anharmonic force fields for the cis and trans conformers of S₁ C₂H₂, and compare the results to experiment. The vibrational assignments of recently observed levels belonging to the cis well are of particular interest. A refined estimate of the cis origin position (44,870?±?10?cm^?1) is proposed, and preliminary low-energy fits to the global J?=?K?=?0 trans level structure are also described. The performance of perturbation theory in this isomerizing system is examined, and both surprising successes and failures are encountered. We examine these and their causes, and offer practical suggestions for avoiding the pitfalls of applying perturbation theory to systems with large amplitude motions.     

Influence of the ordered structure of short-chain polymer molecule all-trans-β-carotene on Raman scattering cross section in liquid

We measured the resonant Raman spectra of all-trans-β-carotene in solvents with different densities and concentrations at different temperatures.The results demonstrated that the Raman scattering cross section(RSCS) of short-chain polymer all-trans-β-carotene is extremely high in liquid.Resonance and strong coherent weakly damped CC bond vibrating properties play important roles under these conditions.Coherent weakly damped CC bond vibration strength is associated with molecular ordered structure.All-trans-β-carotene has highly ordered structure and strong coherent weakly damped CC bond vibrating properties,which lead to large RSCS in the solvent with large density and low concentration at low temperature.     

A density functional study of plutonyl trifluoroacetone complexes in the gas phase and in solution

The results of a density functional study on a plutonyl compound with two trifluoroacetone ligands are presented. Several conformations of the complex have been examined, namely the structure in which the two ligands are in a cis conformation one with respect to the other, in a trans conformation one with respect to the other, and the structure in which the two ligands lie on the same plane. The calculations have been carried out at the local density approximation level of theory. The relative energies of the conformers have been determined and their geometries have been optimized in the gas phase and in an organic solution. The liquid-state environmental effects are included via a simple cavity model and by using the self-consistent reaction field method. This study shows that the trends in stability of the different conformers in the gas and liquid phases are similar and that the most stable conformer has a cis structure.     

Gas phase A-band short time photodissociation dynamics of trans and gauche conformations of 1-iodopropane and comparison with the solution phase short time photodissociation dynamics

A-band resonance Raman spectra are reported for gas phase 1-iodopropane. The gas phase absorption spectrum and resonance Raman intensities were simulated using time-dependent wavepacket calculations and a simple model in order to extract the A-band short time photo-dissociation dynamics for the trans and gauche conformers of 1-iodopropane. The gas phase short time dynamics for trans and gauche are very similar to the results obtained from a reanalysis of corresponding solution phase spectra. This indicates that solvation has little effect on the A-band short time photodissociation dynamics. However, the electronic dephasing parameters for the gauche conformer increase significantly upon solvation while the trans conformer parameters are almost the same in the gas and solution phases. This suggests that the gauche conformer in the A-band excited electronic state undergoes stronger interaction with the solvent than the trans conformer to give rise to faster electronic dephasing upon solvation for the gauche conformer.     

Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. The main objectives have been to follow the dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ^? is approximately perpendicular to the ring plane. Only weak hydrogen bonds are formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bond structure. We also conclude that anionic UQ can be accurately modelled by molecular mechanics methods, but the conformation of the methoxy groups in neutral UQ can hardly be properly modelled using a standard force field.     

Molecular dynamics simulations of plastoquinone in solution

Molecular dynamics simulations of plastoquinone, an important cofactor in the photosynthetic reaction in green plants, are carried out in water solution. Models of both neutral and anionic plastoquinone are built and thoroughly verified. Detailed information concerning spatial distribution of the hydrogen bonds with coordination numbers, together with rotational energetics of the tail in solution are given. The isoprenoid tail was replaced by an ethyl group, which was found to move freely between 0° (cis to the adjacent carbonyl oxygen) and 90° (perpendicular to the quinone ring plane). The results obtained should remove several inconsistencies between earlier experimental and theoretical results to yield a detailed dynamic picture of plastoquinones in solution. Neutral quinones form only a few weak hydrogen bonds to the solvent molecules, while the anionic forms show a distinct solvation structure due to several strong solute-solvent hydrogen bonds. Both the direction and strength of these hydrogen bonds agree well with recent EPR/ENDOR data.     

The cis-effect using the topology of the electronic charge density

We provide a physics-inspired coupling mechanism explaining the cis-effect in terms of electronic and nuclear degrees of freedom and explore the implications for three families of molecules. The cis- or trans-effect is related to the tendency of electronic charge density to move away from the bond critical point (BCP) and towards the associated nuclear attractors. A quantitative measure of this effect is given by the λ ₃ eigenvalue of the Hessian matrix of the electronic charge density. The physical origin of the cis-effect is tied to the observation that the central X=X, X=C or N bond-paths of the cis-isomers are more bent (they are up to 1.5% longer than the internuclear distance) than the bond-paths of the corresponding trans-isomers. Greater bond-path bending is associated with a stronger cis-effect; the direction of bond deformation can in all cases be predicted by the most facile (least compressible) mode of the electronic stress tensor. Further to this, the ellipticity ε of the X=X BCPs of a molecule displaying the cis-effect is lower in the cis-isomer than for the corresponding trans-isomer, suggesting that the cis-effect is less counterintuitive than previously thought. The molecules that exhibit the greatest cis-effect are those with fluorinated double bonds; this is because the most facile modes of the C–F bond couple with the highest-symmetry normal mode of vibration. Qualitative agreement is found with existing experimental data and predictions are made where experimental data is lacking.     

Detailed mechanism of trans–cis photoisomerization of azobenzene studied by semiclassical dynamics simulation

A realistic dynamics simulation study is reported for the trans–cis photoisomerization of azobenzene. The simulation follows both nπ* and ππ* excitations and each excitation is induced by a 50 fs (FWHM) laser pulse. The simulation results show that, for both excitations, the reaction path is predominated by the rotation coordinate of the NN bond. The simulation finds that the CNN inversion angles expand as soon as the rotation starts. The expansion of the CNN bond angles permits the molecule to rotate efficiently. It is therefore suggested that the photoisomerization of trans-azobenzene follows an inversion-assisted rotation path. These simulation results are significant for understanding the mechanism of this important process.     

A DFT study of the mechanism and selectivities of the [3 + 2] cycloaddition reaction between 3‐(benzylideneamino)oxindole and trans‐β‐nitrostyrene

The mechanism and regioselectivities and stereoselectivities of the [3 + 2] cycloaddition (32CA) reaction of 3‐(benzylideneamino) oxindole (AY) and trans‐β‐nitrostyrene have been studied using both B3LYP and ωB97XD density functional theory methods together with the standard 6‐31G(d) basis set. Four reactive pathways associated with the ortho and meta regioselective channels and endo and exo stereoselective approaches modes have been explored and characterized. While the B3LYP functional fails to predict the experimental regioselectivity, the ωB97XD one succeeds to predict the experimentally observed meta regioselectivity favoring the formation of meta/endo cycloadduct as the major isomer. Inclusion of solvent effects increases the regioselectivity and decreases the experimentally observed stereoselectivity. Analysis of the density functional theory global reactivity indices and the Parr functions of the reagents in its ground state allows explaining the reactivity and the meta regioselectivity of this zwitterionic‐type 32CA reaction, which account for the high polar character of this reaction. Non‐covalent interaction analysis of the most favorable meta/endo transition state structure reveals that the formation of a hydrogen‐bond between 1 nitro oxygen and the AY N–H hydrogen is responsible for the selectivity experimentally found in this polar zwitterionic‐type 32CA reaction.