The difluoroethylenes: A reconsideration of the “Cis effect”

Ab initio molecular orbital calculations have been carried out on all three isomers of difluoroethylene with geometry optimization. The calculations were done with a “double-zeta” basis set. After correction of the SCF energies for the effect of electron correlation, the 1,1-isomer is shown to be 8 kcal/mole lower in energy than the cis, which is 1 kcal/mole more stable than the trans. As the stabilization of the isomers increases, the distance between the fluorine atoms decreases: trans, 3.57 Å; cis, 2.77 Å; 1,1-isomer 2.20 Å. A simple explanation for these trends is based upon electrostatics and the small size and high electronegativity of the fluorine atom. As the fluorine atoms come closer together, the destabilization due to nuclear repulsions and electron repulsions is offset by the increased stabilizing electrons-nuclei attractions.     

Conformational analysis of the complexes of copper(ii) with two identical α-amino acid ligands,relative stability of the cis and trans isomers

Conclusions The energy closeness of the cis and trans isomers of the (Ala)₂Cu complexes, and consequently the possibility of the presence of the cis isomers in the equilibrium mixture, was shown. The differences in the energies of the cis and trans isomers increase in the complexes with the N-mono- and N,N-dimethyl-substituted alanine. The coexistence of both isomers is thereby possible for the monosubstituted compounds, but the disubstituted cis isomers are virtually unrealized. According to the conformational calculations, the formation of the optically active compounds containing ligands of one configurational series is more preferred among the complexes considered.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2484–2487, November, 1987.     

Design of a new dihedral-angle-controlled molecular scissors: A DFT investigation

DFT calculations are employed to investigate the effects of the addition of a photoisomerizable stilbene unit to Aida′s molecular scissors on relative energies, dipole moments, and kinetic stability according to HOMO-LUMO energy gaps and amplitude of the open-close motion of blade moieties. The most obvious finding emerging from this study is the coming into existence of a new pair of molecular scissors operated by two photoswitchable units. Based on photoisomerization of azobenzene and stilbene units, four conformations appear for these new molecular scissors: cis–cis, cis–trans, trans–cis, and trans–trans. The HOMO-LUMO energy gaps promise that all isomers are kinetically stable. The other important finding is that in these new molecular scissors the dihedral angle between the two blade moieties can be controlled and measured through the open-close motion and the blade parts can adopt two middle states in addition to open-close forms.     

Three- and four-center trans effects in triply bonded ditungsten complexes: an ab initio molecular dynamics study of compounds with stoichiometry W2Cl4(NHEt)2(PMe3)2

We have performed ab initio molecular dynamics simulations based on density functional theory to characterize the structural, electronic, and dynamic properties of the three major isomeric forms of the title compound. In agreement with experimental results, calculations with two different parametrizations of the exchange-correlation functional (BLYP and BP) both indicate the cis-C2 form as the most stable isomer. The relative energies of the different forms are, however, small (less than approximately 1-2 kcal/mol), and the three compounds show overall very similar ground-state properties. Larger differences exist in their finite temperature behavior, which is dominated by the facile dissociation of one or both phosphine ligands. The calculated activation energies for phosphine dissociation differ clearly for the trans and the cis isomers and vary in the order trans < cis-C2 less than approximately cis-Ci. Analysis of the electronic structure of the transition states shows that the difference in activation energy between cis and trans isomers can be rationalized in terms of a classic trans effect caused by a molecular orbital spanning the three atomic centers N-W-P. The subtle difference between the two cis isomers, on the other hand, is likely due to an analogous four-center trans effect N-W-W-P which is mediated via metal-metal orbitals and involves ligands on both tungsten atoms.     

UV-, VIS- and IR-light-induced isomerization of HSNO in a low-temperature matrix

An infrared spectroscopic investigation has been performed on the trans and cis isomers of thionitrous acid (HSNO) and their D- and ¹⁵NO-isotopic modifications in argon matrices at 12 K. The substances were prepared photolytically from thionylimide (HNSO) isotopes in the matrix. With UV (250 nm), VIS (585 nm), and IR irradiation the cis → trans or the trans → cis isomerization of HSNO was induced, allowing an unequivocal distinction between the closely resembling IR spectra of the trans and cis isomers. Complete sets of fundamental frequencies of both rotamers were obtained and assigned by normal coordinate analysis using the transferable valence force field (TVFF) approach. Parallel to this analysis ab initio calculations on the SCF- and CI-levels were performed to predict energy, geometry, and barrier of internal rotation for the two HSNO rotamers.     

An ab initio MO study on the structures and electronic states of hydrogen-bonded O3- HF and SO2-HF complexes

Ab initio molecular orbital (MO) calculations have been carried out for base-hydrogen fluoride (HF) complexes (base = O3 and SO2) in order to elucidate the structures and energetics of the complexes. The ab initio calculations were performed up to the QCISD(T)/6-311++G(d,p) level of theory. In both complexes, hydrogen-bonded structures where the hydrogen of HF orients toward one of the oxygen atoms of bases were obtained as stable forms. The calculations showed that cis and trans isomers exist in both complexes. All calculations for the SO2-HF complex indicated that the cis form is more stable in energy than the trans form. On the other hand, in O3-HF complexes, the stable structures are changed by the ab initio levels of theory used, and the energies of the cis and trans forms are close to each other. From the most sophisticated calculations (QCISD(T)/6-311++G(d,p)//QCISD/6-311+G(d) level), it was predicted that the complex formation energies for cis SO2-HF, trans SO2-HF, cis O3-HF, and trans O3-HF are 6.1, 5.7, 3.4, and 3.6 kcal/mol, respectively, indicating that the binding energy of HF to SO2 is larger than that of O3. The harmonic vibrational frequencies calculated for cis O3-HF and cis SO2-HF complexes were in good agreement with the experimental values measured by Andrews et al. Also, the calculated rotation constants for cis SO2-HF agreed with the experiment.     

Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.     

Theoretical Studies of Distyrylbenzene and its Optical Properties

The electronic and geometrical properties of distyrylbenzene (DSB) are investigated by using chemistry theoretical calculation methods. Specifically, the excited state properties are studied by performing ab initio correlation interaction singlet (CIS) and time‐dependent density functional theory; the ground state and Raman activities are computed by density functional theory with the B3LYP method. Eight conformers of distyrylbenzene are found and they are derived from three isomers which are cis, cis‐, cis, trans‐, and trans, trans‐, respectively. The relative energy shows that each isomer of three types is separated with a large energy barrier, but a small energy difference of each conformer is found if they are in the same type. The transition state also shows the barrier between conformers is lower than isomers. The computed excited transition energies using ZINDO/S based on the optimized geometries at a DFT/B3LYP level with 6–31+G show an excellent agreement with experimental absorption spectra.     

Theoretical studies of cyclopropylsilylenes: The structures and stability of cyclopropylsilylene C3H5SiH

Ab initio molecular orbital calculations at the G2(MP2) level have been carried out on cyclopropylsilylene C₃H₅SiH. Four equilibrium structures were located. Like H₂Si, the ground state of C₃H₅SiH is singlet and the triplet is the low‐lying excited state. The singlet–triplet separation energy is 127.9 kJ/mol. The cis‐trans isomerization path of singlet cyclopropylsilylene was investigated by intrinsic reaction coordinate (IRC) calculations. The calculations show that no gauche conformers exist along the potential energy curve of the cis‐trans isomerization and the isomerization happens with a barrier of 30.1 kJ/mol. Changes (ΔH and ΔG) in thermodynamic functions, equilibrium constant K(T), and A factor and reaction rate constant k(T) in Eyring transition state theory of the cis‐trans isomerization were also calculated. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Probing highly efficient photoisomerization of a bridged azobenzene by a combination of CASPT2//CASSCF calculation with semiclassical dynamics simulation

Mechanism of phototriggered isomerization of azobenzene and its derivatives is of broad interest. In this paper, the S(0) and S(1) potential energy surfaces of the ethylene-bridged azobenzene (1) that was recently reported to have highly efficient photoisomerization were determined by ab initio electronic structure calculations at different levels and further investigated by a semiclassical dynamics simulation. Unlike azobenzene, the cis isomer of 1 was found to be more stable than the trans isomer, consistent with the experimental observation. The thermal isomerization between cis and trans isomers proceeds via an inversion mechanism with a high barrier. Interestingly, only one minimum-energy conical intersection was determined between the S(0) and S(1) states (CI) for both cis → trans and trans → cis photoisomerization processes and confirmed to act as the S(1) → S(0) decay funnel. The S(1) state lifetime is ～30 fs for the trans isomer, while that for the cis isomer is much longer, due to a redistribution of the initial excitation energies. The S(1) relaxation dynamics investigated here provides a good account for the higher efficiency observed experimentally for the trans → cis photoisomerization than the reverse process. Once the system decays to the S(0) state via CI, formation of the trans product occurs as the downhill motion on the S(0) surface, while formation of the cis isomer needs to overcome small barriers on the pathways of the azo-moiety isomerization and rotation of the phenyl ring. These features support the larger experimental quantum yield for the cis → trans photoisomerization than the trans → cis process.     

Chromatographic analysis of cis/trans carotenoid isomers.

Cis/trans configurations of carotenoids are known to effect the biochemistry of carotenoids in certain situations. Methodology for separating carotenoid cis/trans isomers is of importance to nutritionists and food scientists because cis isomers of provitamin A carotenoids have lower provitamin A activities than the all-trans form. Traditional food processing and preservation methods, especially thermal treatments, induce the formation of cis isomeric forms. However, many challenges, are apparent for identifying and analyzing cis/trans isomers present in foods and other biological tissues. The development of current chromatographic methods for the separation of carotenoid cis/trans isomers is reviewed. For the separation of beta-carotene isomers, most procedures employ either Ca(OH)2 or Vydac C18 columns. In general, polymeric C18 columns allow for the detection of cis carotenes, while monomeric C18 columns provide for some separation of certain xanthophylls. The main cis isomers detected in foods are the 13-cis and 9-cis forms, although other forms have also been found (mainly 15-cis and various di-cis isomers). More studies involving the metabolism and physiological consequences of cis/trans isomers in the diet are needed. However, due to limitations in current techniques, further method development in the area of separation, detection and quantitation of cis/trans carotenoid isomers will be required.     

Spectroscopic Characterization of the Geminal Isomer of Lewisite

Abstract

Lewisite is generally a mixture of several components with the trans isomer of lewisite being the predominant compound. A geminal isomer has not been previously reported as one of the components of the mixture. In the lewisite samples we examined, the geminal isomer, dichloro(l-chlorovinyl)arsine, comprised 2.7 per cent of the total material compared to 95.2 and less than 1 per cent, respectively, for the trans and cis isomers. The remaining fraction was not identified. The geminal isomer of lewisite has been characterized along with the trans and cis isomers using several spectroscopic techniques. Proton NMR of the geminal isomer produced a coupling constant consistent with vinylic protons in a geminal configuration. Mass spectrometry and infrared spectroscopy characterizations were based on an ethanedithiol derivative of the lewisite isomers with gas chromatography used to first separate the derivatized isomers. The electron ionization massspectra of the trans and cis derivatives were very similar, but significant differences were observed in the mass spectrum of the geminal form. Infrared absorption spectra were obtained for the trans and geminal derivatives with significant differences observed between the two, but the method was not sensitive enough to detect the cis isomer.

     

A theoretical study of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods

The conformational potential energy surface as a function of the two internal torsion angles in C-nitrosomethanol has been obtained using the semiempirical AM1 method. Optimized geometries are reported for the local minima on this surface and also for the corresponding points on the HF/6-31G, 6-31G*, and 6-31G** surfaces. All methods predict cis and trans minima which occur in degenerate pairs, each pair being connected by a transition state of C_s symmetry. The AM1 structures are found to compare well with the corresponding ab initio structures. Ab initio HF/6-31G and HF/6-31G* harmonic vibrational frequencies are reported for the cis and trans forms of nitrosomethanol. When scaled appropriately the calculated frequencies are found to compare well with experimental frequencies. The ab initio calculations predict the energy barrier for cis → trans isomerization to be between 5.8 and 6.5 kcal/mol with the trans → cis isomerization barrier lying between 2.3 and 6.5 kcal/mol. The corresponding AM1 energy barriers are around 1 kcal/mol lower in energy. The ab initio calculations predict the barrier to conversion between the two cis rotamers to be very small with the AM1 value being around 1 kcal/mol. Both AM1 and ab initio calculations predict interconversion between trans rotamers to require between 1.2 and 1.4 kcal/mol.     

Conformational profile of a proline-arginine hybrid

The intrinsic conformational preferences of a new nonproteinogenic amino acid have been explored by computational methods. This tailored molecule, named ((β)Pro)Arg, is conceived as a replacement for arginine in bioactive peptides when the stabilization of folded turn-like conformations is required. The new residue features a proline skeleton that bears the guanidilated side chain of arginine at the C(β) position of the five-membered pyrrolidine ring, in either a cis or a trans orientation with respect to the carboxylic acid. The conformational profiles of the N-acetyl-N'-methylamide derivatives of the cis and trans isomers of ((β)Pro)Arg have been examined in the gas phase and in solution by B3LYP/6-31+G(d,p) calculations and molecular dynamics simulations. The main conformational features of both isomers represent a balance between geometric restrictions imposed by the five-membered pyrrolidine ring and the ability of the guanidilated side chain to interact with the backbone through hydrogen bonds. Thus, both cis- and trans-((β)Pro)Arg exhibit a preference for the α(L) conformation as a consequence of the interactions established between the guanidinium moiety and the main-chain amide groups.     

An Ab initio study on the conformations of protonated,neutral, and deprotonated amidine

Ab initio SCF molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(?NH)NH₂], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine ?NH is preferred over the –NH₂ site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN?CN cis and trans isomers, respectively, while all the stable HC(NH₂)₂⁺ and HC(NH)₂^? species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C—N single-bond rotation in HC(?NH)NH₃⁺, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN?CN isomers, respectively.     

Separation and identification of various carotenoids by C30 reversed-phase high-performance liquid chromatography coupled to UV and atmospheric pressure chemical ionization mass spectrometric detection.

In this paper the application of on-line HPLC-UV-APCI (atmospheric pressure chemical ionization) mass spectrometry (MS) coupling for the separation and determination of different carotenoids as well as cis/trans isomers of beta-carotene is reported. All HPLC separations were carried out under RP conditions on self-synthesized polymeric C30 phases. The analysis of a carotenoid mixture containing astaxanthin, canthaxanthin, zeaxanthin, echinenone and beta-carotene by HPLC-APCI-MS was achieved by scanning the mass range from m/z 200 to 700. For the characterization of a sample containing cis/trans isomers of beta-carotene as well as their oxidation products, a photodiode-array UV-visible absorbance detector was used in addition between the column and the mass spectrometer for structural elucidation of the geometrical isomers. The detection limit for beta-carotene in positive-ion APCI-MS was determined to be 1 pmol. In addition, an extract of non-polar substances in vegetable juice has been analyzed by HPLC-APCI-MS. The included carotenoids could be identified by their masses and their retention times.     

Improved identification of conjugated linoleic acid isomers using silver-ion HPLC separations

Silver-ion high-performance liquid chromatography (Ag+-HPLC) has been shown to be effective in the resolution of most of the isomers of conjugated octadecadienoic acids (18:2), also known as conjugated linoleic acid (CLA). The CLA isomers identified in natural fats from ruminants are a mixture of numerous positional and geometric isomers from 7,9- to 12,14-18:2. Ag+-HPLC separates both geometric (trans,trans < cis/trans < cis,cis) and positional CLA isomers using the mobile phase hexane/acetonitrile (99.9:0.1). The elution volumes for the CLA isomers were not only affected by the concentration of acetonitrile (in the prepared mobile phase) but also with successive runs during the day using a prepared mobile phase batch, due to the partial solubility of acetonitrile in hexane. However, this drift does not affect the relative resolution of the CLA isomers. The addition of diethyl ether to the mobile phase partly stabilizes the solvent mixture. In order to facilitate the interpretation of Ag-+HPLC chromatograms, the relative retention volumes (RRV) were calculated for each CLA isomer. Toluene was added to all the test portions and served as an estimator of dead volume, whereas the elution of the ubiquitous 9c,11t-CLA isomer was chosen as unity (1.00). Expressing the elution of all the CLA isomers as their RRV greatly helped to standardize each CLA isomer, resulting in relatively small coefficients of variation (% CV) for the trans,trans (<1.5%) and cis/trans (<0.5%) CLA isomers. The identification of the CLA isomers was further facilitated by synthesis of authentic CLA isomers. All the geometric CLA fatty acid methyl esters (FAME) from positions 6,8- to 13,15-CLA were commercially available or synthesized by a combination of partial hydrazine reduction of known polyunsaturated fatty acids followed by alkali isomerization, isolation of products, and further iodine-catalyzed geometric isomerization. Based on expressing the elution volume as RRV and the availability of the synthetic CLA isomers, a unique reversal of the elution order of the c/t CLA isomers was found. It is also proposed that the retention times of CLA isomers by gas chromatography (GC) should be expressed as their relative retention times (RRT) relative to methyl gamma-linoleneate. The availability of CLA reference materials and the application of RRV and RRT to Ag+-HPLC and GC separations, respectively, will greatly improve in the identifications of CLA isomers.     

Coexistence of two isomers in the crystal of 1,5-dihydro-1,5-dimethyl-3,3,7,7-tetraphenylcyclotetrasiloxane

Crystal and molecular structure of the title compound has been determined. The structure disordering has been detected which can be considered as a result of coexistence of two isomers (cis and trans, each in two conformations) in the crystal.     

Overview of methods for the determination of trans fatty acids by gas chromatography, silver-ion thin-layer chromatography, silver-ion liquid chromatography, and gas chromatography/mass spectrometry

trans Isomers of naturally occurring cis-unsaturated fatty acids are produced when liquid vegetable oils or marine oils are partially hydrogenated to produce margarine, shortenings, and other hardened-fat products. Isomeric trans fatty acids are also formed in the intestinal tract of ruminants, and they appear in small amounts in dairy products and ruminant meat. Currently, satisfactory analyses for the fatty acid profiles of fats containing trans fatty acids are obtained by gas chromatography (GC) using capillary columns coated with highly polar cyanosilicone stationary phases. In capillary GC methods, the key limitation has been the incomplete separation of trans-monoenoic acid isomers from their cis isomers; however, recent reports have demonstrated that improvements in separation are attainable with the use of 100 m columns. In these columns, there is very little overlap of cis and trans isomers. More accurate trans fatty acid analyses can be obtained by coupling GC with either silver-nitrate thin-layer chromatography or silver-nitrate liquid chromatography.