Conformational and NBO analysis on cis and trans isomers of methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylate

The cis and trans-methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylates were prepared and ¹H and ¹³C NMR spectra were recorded for both isomers. Conformational and NBO analysis were carried out for the cis and trans isomers. Conformer structures were pre-optimized using the hybrid method B3LYP along with the 6-311+G(d) basis set. Frequency calculations were employed to confirm the structures as minimum points. Potential energy surfaces (PES) were built at the same level of theory. Geometries obtained from DFT calculations were used to perform NBO analysis by the NBO 3.1 module in GAUSSIAN 03. The results obtained through theoretical calculations revealed that the shielding observed at C1 for the trans isomer can be attributed to carbomethoxy γ-effect, together with the hyperconjugative effect, while only hyperconjugative effects were found to explain the shielding of C3. The higher chemical shift value of C3 of the cis isomer was attributed to the carbonyl substituent, which plays an important role by capturing part of the electronic density in C3.     

Reactivity of ruthenium complexes with uninegative (X,S)-donor ligands (X = S,P)—II. Phosphine substitution in [Ru(S,S)2(PR3)2] derivatives. Crystal structure of trans-bis(O-ethyldithiocarbonate)bis(dimethylphenylphosphine)-ruthenium(II)

The complexes [Ru(S,S)₂(PPh₃)₂] [S,S = EtCOCS₂⁻, (CH₂)₄NCS₂⁻] react with a variety of tertiary phosphines with the substitution of triphenylphosphine and the formation of [Ru(S,S)₂(PR₃)₂]. The reaction occurs with the formation ofthe cis isomer, except for the complex with PMe₂Ph that gives rise to the trans isomer as the crystal structure shows. The effect of the different phosphines on the ruthenium complex is analysed in terms of the spectroscopic and electrochemical properties of the isolated compounds. The cyclic voltammetric studies of the cis complexes show that isomerization to the trans isomer occurs on oxidation. This isomerization is not observed in the trans-[Ru(S,S)₂(PMe₂Ph)₂] complexes that give rise to stable trans-ruthenium(II)/ruthenium(III) couples. In a similar way the diphosphine complexes afford a quasi-reversible cis-ruthenium(II)/ruthenium(III) process.     

Photodynamics of azobenzene in a hindering environment

We have run trajectory surface hopping simulations of the trans → cis photoisomerization of azobenzene, subject to a pulling force. The model mimics two situations: a trans-azobenzene derivative with bulky substituents that may not be easily displaced, and a recent experiment by Gaub’s group [T. Hugel, N.B. Holland, A. Cattani, L. Moroder, M. Seitz, H.E. Gaub, Science 296 (2002) 1103; N.B. Holland, T. Hugel, G. Neuert, A. Cattani-Scholz, C. Renner, D. Oesterhelt, L. Moroder, M. Seitz, H.E. Gaub, Macromolecules 36 (2003) 2015; G. Neuert, T. Hugel, R.R. Netz, H.E. Gaub, Macromolecules 39 (2005) 789], in which a polymer with azobenzene units was stretched in an atomic force microscope. In both cases, the shortening of the azobenzene moiety in going from the trans to the cis form is opposed by a pulling force. Our simulations show that the trans → cis photoconversion is only partially suppressed by considerably large forces (≈500 pN or more). However, the cis isomer reverts to trans in the ground state, with the help of the pulling force and using the vibrational energy that is available in the first 1–2 ps. The lowering of the quantum yields is therefore the combined result of hindering of the excited state process and of the hot ground state back reaction.     

Trans-cis isomerization of an azoxybenzene liquid crystal

Trans-cis isomerization was investigated in a room temperature liquid crystal mixture of two azoxybenzene compounds. Experiments were performed on isolated molecules in dilute solutions and on the liquid crystal phase composed of the pure compounds. The absorption spectra of the trans and cis isomers were found to be similar to those of azobenzene compounds, as were the birefringence and order parameter of the nematic liquid crystal phase. The photo-optic properties were also similar in that irradiation by ultraviolet light caused the conversion from trans to cis isomers, while short wavelength visible light incident on these compounds resulted in the conversion from cis to trans isomers. The activation energy for thermal relaxation from the cis to trans isomer in the liquid crystal phase was determined to be (66±7) kJ/mole, which is less than for azobenzene in solution. While a photostationary state in a dilute solution with approximately equal numbers of trans and cis isomers was achieved, the nematic-isotropic transition of the mixture of the pure compounds decreased from 70°C to room temperature with a cis concentration of only about 12%. One unusual finding was that the photostationary concentration of trans and cis isomers due to irradiation with light of a specific visible wavelength depended on the starting concentrations of the two isomers, indicating that there may be a molecular conformation that is not photo-responsive and relaxes only thermally.     

X-ray diffraction studies on cis- and trans-4'-cyanobiphenyl-4-yl 3-n-propylcyclobutane-1-carboxylate

X-ray diffraction has been used to study the nematic phases of the cis and trans isomers of an elongated molecule containing the cyclobutane group. It has been shown that these nematic phases consist of a mixture of single molecules and overlapping core dimers. It has been found that increasing the temperature of the cis isomer rapidly reduces the dimer population, whereas increasing the temperature of the trans isomer enhances the dimer population. This provides an explanation of the relatively high clearing temperature of the trans isomer. The different temperature dependences of the dimer population in the cis and trans isomers has been explained by a model involving inversion of the cylobutane group.     

Synthesis and structure of novel heterocyclic aminotelluranes

A series of novel 6-alkoxy-12H, 14H-[1,2,3]benzoxatellurazino[2,3-b]-[1,2,3]benzoxatellurazines 3 was synthesized from tetraalkoxytelluranes and bis(2-hydroxybenzyl)amines. ¹H, ¹³C and ¹²⁵Te NMR studies suggest that these aminotelluranes, unlike their orthoamidoester analogs, have a rigid trans-fused conformation. A preferential trans-fused conformation was also deduced from ab initio MO calculations of a model oxatellurazinooxatellurazine 7, using the STO-3G and SBK basis sets, and the Gaussian-92 program, which imply that the trans-fused aminotellurane is more stable than the corresponding cis isomer by 10.3 kcal/mol.     

Multidimensional anharmonic calculation of the vibrational frequencies and intensities for the trans and cis isomers of HONO with the use of normal coordinates

The equilibrium geometry and the potential energy and dipole moment surfaces have been determined for the cis and trans isomers of the HONO molecule by an ab initio Moller–Plesset (MP2) calculation with a wide set of atomic orbitals. The multidimensional anharmonic vibrational Schrodinger equations are solved using the variational method with the Hamiltonian and wave functions written in the normal coordinates of cis and trans isomers. All one- and two-dimensional and a number of three-dimensional vibrational problems are solved to obtain the energy levels and vibrational eigenfunctions. The frequencies and intensities for the fundamental, overtone and some combination bands are determined in good agreement with the available experimental results. The calculation shows the strength of coupling between different vibrational modes and reveals the presence of strong resonances between the (v₁, v₃, v₆) and (v₁, v₃−1, v₆+2) states of cis-HONO. This fact may be important for understanding the energy redistribution between the intermolecular degrees of freedom. The magnitude and direction of vibrationally averaged ground-state dipole moment of both isomers, as well as the direction of transition dipole moments, are in good agreement with the experimental findings. The changes in the values of dipole moment and some geometrical parameters of cis- and trans-HONO on vibrational excitation are also computed.     

Stereocontrolled synthesis of (RR)- and (RS)-5-hydroxy-2-methylhexanoic acid lactones : Pheromone of the carpenter bee via palladium-catalyzed reactions

(E,Z)-2,4-Hexadiene was transformed to the lactone cis-1 ( 93% cis)(pheromone of the carpenter bee) in a stereospedfic reaction sequence via a Pd-calalyzed 1,4-acetoxychlorination. The same reaction sequence applied to (E,E)-2,4-hexadiene afforded the isomeric lactone trans-1 (91% trans).     

Peptide models XXIX. cis–trans Isomerism of peptide bonds: ab initio study on small peptide model compound; the 3D-Ramachandran map of formylglycinamide

Thermodynamic separations for cis and trans-amides and formylglycinamide range from 0.00 to 4.77 kcal/mol as computed at various levels of theory. The barriers for trans→cis-isomerization, for the same set of compounds, computed at various levels of theory, were found between 15.69 and 22.67 kcal/mol. The cis- and trans-Ramachandran maps of formylglycinamide are compared and the topology of the ab initio 3D-Ramachandran map is presented for the first time.     

An ab initio potential energy surface for the υ4 vibrational mode of hydrogen peroxide

In this paper, the levels and the torsional microstates of hydrogen peroxide are determined from fully optimized ab initio calculations using a nuclear model in one dimension. Calculations have been performed at the MP2 level with the 6-311 G(2df,2pd), 6-31 1+G(2df,2pd), cc-pVTZ and AUG-cc-pVTZ basis sets including polarization orbitals and diffuse functions. The most stable conformation, calculated with the MP2/AUG-cc-pVTZ approach, is a trans–gauche conformer lying at 67.5° from the trans structure. By using the same level of calculations, the heights of the trans and cis barriers have been determined to be 386.5 and 2643.8 cm⁻¹ in a good agreement with the experimental data. The variational torsional levels split into four components by the tunnelling effect of the barriers. The splitting of the fundamental level caused by the trans barrier has been found to be 11.8683 cm⁻¹, whereas the splitting caused by the cis barrier is insignificant under n=2. Current ab initio energies confirm the experimental assignments and verify the separability of the torsion from the rest of the vibrations. However, the experimental relation of dependence on the torsion of the rotational constants cannot be reproduced in one-dimension and depends on several additional vibrational effects.     

Isomeric complexes of ruthenium(II) with neutral heterocyclic schiff base ligands. High resolution proton resonance spectra of trans-cis isomeric pairs of RuX2L2 (L = 2-arylpyridinecarboxaldimine, X = Cl, Br) and comparison of their physical properties

The reaction of 2-arylpyridinecarboxaldimine [RH₄C₆NC(H)Py, L (1)] with hydrated RuX₃ (X = Cl, Br) in boiling C₂H₅OH affords dark crystals of RuX₂L₂. Two geometrical isomers of the compound have been isolated and characterized by analytical and spectroscopic data. The trans isomer of RuCl₂L₂ shows a single sharp band for ν(Ru---Cl), whereas two bands are observed for the corresponding cis isomer. The highresolution ¹H NMR spectra of the isolated complexes are reported and completely assigned. All the complexes have multiple t₂→π^*(L) transitions in the visible region. Each of the complexes display a quasi-reversible oxidative response due to an Ru^III/Ru^II couple in the range 0.25–0.40 V vs S.C.E. at a platinum working electrode. The formal potentials of this couple obey the Hammett relationship. The ligand-based irreversible oxidations are also briefly noted.     

Proton magnetic resonance studies of cyclic compounds—III cis- and trans-2,6-dimethylmorpholines

Commercial 2,6-dimethylmorpholine has been separated into cis- and trans-isomers by vapour phase chromatography. The PMR spectra of the bases, analysed as ABXK₃ systems (J_AK = J_BK = 0), show that the most abundant isomer has the cis-configuration, consisting probably of a single conformation in which both methyl groups are equatorial. The trans-isomer is probably a mixture of rapidly inverting and energetically equivalent conformations, since the vicinal coupling constants deduced from the PMR spectrum are averages of those expected for the two conformations.     

Use of ab initio computational results and experimental frequencies to construct the internal rotational potential function for acrolein

Ab initio optimizations of the complete acrolein molecular geometry accomplished using analytical gradient methods at the 6-31G* SCF level at ten points during rotation from the planar trans- to the planar cis-form (rotation about the single C---C bond) are used to calculate the values of the Pitzer function F(φ), the coefficients of its Fourier expansion, and the coefficients in the potential energy expansion. The theoretical potential expansion coefficients are then adjusted using the experimental torsional frequencies and their overtones for the trans- and cis-forms of CH₂=CH---CH=O and CH₂=CH---CD=O. For the cis-conformer two different sets of experimental frequencies are employed. The dependence of the slope of the acrolein potential energy curve on the experimental frequency set used for the cis-rotamer is discussed.     

Deuterium NMR studies of inositol liquid crystals [1]

Deuterium NMR investigations are presented on members of two new mesogenic series derived from the naturally occurring stereoisomers myo- and scW/o-inositol. Tetraethers of these two series exhibit thermotropic columnar phases in which the columns are apparently formed by stacked hydrogen bonded dimers of these molecules which chemically are vicinal diols. Deuterium NMR measurements were performed on the tetraoctyl homologues 2e (a cis diol) and 3e (a trans diol) of these series. We have investigated mixtures of these diols with small amounts of benzene-d₆ as probe molecules as well as samples of the neat diol compounds deuteriated at their hydroxyl groups. The results obtained show that the mesophases of both compounds are uniaxial and align partially in a magnetic field upon slow cooling from their isotropic liquids. The alignment is with the director parallel to the field direction indicating that the anisotropic magnetic susceptibility of this mesophase is positive. The deuterium quadrupole splitting of the benzene-d₆ probe in both systems is temperature dependent and in the trans diol 3e it even changes sign. This is interpreted in terms of a model in which the benzene-d₆ probe equilibrates rapidly between two (or more) solvation sites with quadrupole splittings of opposite signs The deuterium spectra of the neat deuterium labelled cis diol 2e exhibit two different signals due to the two deuterons which are located at the axial and equatorial hydroxyl groups. This indicates that there is no fast intra- or intermolecular exchange of the hydroxyl hydrogens. The overall quadrupole splittings of the hydroxyl deuterons in this compound are highly reduced compared to their static values and this is interpreted in terms of motional modes involving both reorientation of the hydroxyl deuterons about their C-O axis and overall reorientation of the molecules (or pairs of molecules) around the columnar axes. The corresponding spectra of the neat deuteriated trans diol 3e exhibit a single spectrum indicating that both hydroxyl deuterons in this compound are equivalent, or very nearly so. Within the mesophase region the spectrum undergoes gradual changes due to the increase in the molecular mobility, but the overall motional narrowing is less than in the cis isomer 2e. Apparently due to stronger hydrogen bonding in the trans isomer 3e the precession of the hydroxyl groups is hindered and a fast molecular reorientation is only possible at high temperatures.     

A comparative ab initio study of the geometry and force field of thionformic acid with formic and thiolformic acids

The energy and force field for the planar cis and trans conformers of thionformic acid have been calculated using the 4–31 G basis set, augmented by a complete set of d-functions on the sulfur atom, with full geometry optimization. Extensive comparisons are made between the changes in geometry and selected force constants in going from cis- (chain) to the trans- (ring) structures of thionformic, thiolformic and formic acid. These changes are discussed in terms of a hydrogen bonding type of interaction in the O---HS, S---HO and O---HO structural units respectively. Of the thioacid conformers, the trans-thiol is found to be the most stable; the trans-thion and cis-thiol both about 10 kJ mol⁻¹ less stable; and the cis-thion the least stable by about 38 kJ mol⁻¹.     

Coordination geometry of chromium(VI) species. The first example of cis-bridging chromate ions in helically structured catena(μ-CrO4-O,O′)[Ni(HIm)3H2O]

Nickel(II) chromate complex with imidazole (HIm) was isolated from the [Ni²⁺–HIm–CrO₄²⁻] system in various experimental conditions, i.e. reagent molar ratios and nickel(II) salts. The catena(μ-CrO₄-O,O′)[Ni(HIm)₃H₂O] (1) crystallizes in monoclinic crystal system—space group P2₁/n with cell parameters: a=11.784(2), b=8.899(2), c=13.934(3) (Å), β=95.19(3) (°). The unit cell contains two independent helixes, left- and right-handed, stabilized by intrahelical and interhelical hydrogen bonds (HB) and π–π interactions. The cis coordination of the CrO₄²⁻ anions and the HB systems appeared to be the main determinants of the helical architecture. To the best of our knowledge the cis-chromate coordination was observed for the first time. The cis coordination causes the distortion of the nickel octahedron, which was analysed by 4 K single crystal electronic spectra with D_4h symmetry approximation (gaussian resolution and crystal field parameters). This symmetry was also confirmed with the polarised electronic spectra. The magnetic properties of the complex suggest the occurrence of weak intrachain antiferromagnetic interactions between the magnetic Ni^II center. The computational DFT studies of complex 1 assuming three possible isomers mer[(HIm)₃]–cis[(CrO₄²⁻)₂], mer–trans and fac–cis suggested that the main contribution to the stability of 1 might have interhelical and intrahelical hydrogen bonds.     

Construction and investigation of photo-switch property of azobenzene-bridged pillar[5]arene-based [3]rotaxanes

Series of azobenzene-bridged pillar[5]arene-based [3]rotaxanes with different alkyl chain length of guest molecules were constructed by threading-endcapping method with alkylenetriazole as axile and tetrahydrochromene as endcapping group.The encapsulation of pillar[5]arenes were proved by highresolution mass,¹ H NMR and NOESY spectra.The photo-responsive property were examined by irradiation of the synthesized [3]rotaxanes with 365 nm and blue light LED,which caused trans to cis and cis to trans isomerization,respectively.Irradiation of corresponding model guest compounds without pillar[5]arene encapsulation resulted in near completely trans to cis and cis to trans isomerization,indicating the existence of pillar[5]arenes is the determining factor for the comprised photo isomerization efficiency.     

Molecular modeling of the olefin metathesis by tungsten(0) carbene complexes

Density functional and second-order Moller–Plesset theory were used to model W(0) carbene mediated homogeneous metathesis reaction of propylene. The calculations show that the rate determining step of the metathesis is the initiation. After the initiation has been completed the rate determining step becomes dissociation of olefin–metallocarbene complex. The low stereoselectivity of the olefin metathesis reaction is due to the close matching of activation energies for cis and trans isomer formation and the fast cis–trans isomerization caused by the catalysts. The non-productive olefin metathesis reaction always dominates the reaction mixture owing to its very low activation energy. The electronic structure of metal carbene olefin complexes can be described as a combination of donor–acceptor interactions between HOMO of the olefin and LUMO of metal carbene located at carbene carbon on the one hand, and the Dewar, Chatt and Duncanson back donation scheme on the other.     

Potential constants and Coriolis coupling constants of perhalogenated ethylenes: Part 3. trans-ClFC=CFCl, trans-ClBrC=CBrCl and trans-FBrC=CBrF

Based on vibrational frequencies a calculation of a general quadratic force field has been carried out for trans-ClFC=CFCl, trans-ClBrC=CBrCl and trans-FBrC=CBrF via an iterative method. The resulting transformation L matrices were used to evaluate the Coriolis coupling constants and these were used to calculate inertial defects. The calculated values of the inertial defects are lower than those of the respective cis-ethylene-type molecules.     

Cyclopropyl carbanions derived from esters of 2-phenylcyclopropylcarboxylic acids: Configurational stability and reaction with electrophiles

The base-catalyzed cis-trans isomerization of cis and trans-alkyl 2-phenylcyclopropylcarboxylates was studied in several aprotic solvents. It was found that contact ion-pain of the derived carbanion lithium salts were configurationally more stable than the solvent-separated ones. Reaction of either the cis or the trans esters with MeI, and the reaction of the cis ester with Ph₂C = O, resulted in the corresponding I-substituted derivatives having cis geometry only. This was explained as due to steric hindrance to elctrophilic attack exerted by the 2-phenyl group in the case of the trans substrate. The trans esters did not react with Ph₂C=O. Inhibition of the trans-to-cis isomerization of the carbanion salt of the trans substrate in presence of Ph₂C=O could lead to this result.