Theoretical study of the N---H tautomerism in free base porphyrin

The N---H tautomerism of free base porphyrin is investigated at the semiempirical spin-unrestricted AM1 (UAM1) and ab initio RHF/3-21G levels. The UAM1 method provides delocalized geometries for all stationary structures without imposing any symmetry constraint. RHF/3-21G geometry optimizations have to be performed under symmetry restrictions to ensure that realistic delocalized structures are obtained. Both the semiempirical and the ab initio calculations predict that the interconversion between trans tautomers proceeds in an asynchronous two-step process via intermediate cis tautomers. The cis tautomers are characterized as minima in the potential energy surface and are 8–10 kcal mol⁻¹ higher in energy. The activation energy for the trans → cis interconversion is calculated to be approximately 23 kcal mol⁻¹ at the 3-21G level. The activation energy for the synchronous trans → trans interconversion is higher and has a value of 30.5 kcal mol⁻¹. The activation energies obtained at the semiempirical UAM1 level are twice as large as the ab initio values.     

Novel starshaped initiators for the controlled radical polymerization based on resorcin[4]- and pyrogallol[4]arenes

Multifunctional macrocyclic initiators for the atom transfer radical polymerization (ATRP) based on different resorcin[4]- and pyrogallol[4]arenes have been synthesized. The initiators with 8, 12 and 16 tertiary -bromoesters on the core were received by complete esterification of all phenolic groups with 2-bromo-isobutyryl bromide. The calixarene derivatives with aliphatic chains on the bridging methine carbon were obtained as their rccc (all cis) isomers, while the corresponding calixarenes with aromatic substituents gave mixtures of their rccc and rctt (cis, cis, trans, trans) isomers.     

The vibrational spectra, molecular structure and conformation of organic azides : Part IV. An ab initio study of hydrazoic acid, azidomethane, azidoethane, azidoethene and azidomethanal

Fully optimized geometries have been calculated for the title compounds at the Hartree—Fock SCF level and compared with existing experimental data. A basis set of double zeta quality has been employed. For hydrazoic acid, a calculation with a larger basis set, expected to give results near the Hartree—Fock limit, has also been performed. All of the calculations show the azide group to be slightly bent with a trans configuration around the central NN bond. Azidoethane is predicted to exist in two conformations, gauche (71°) and anti, with a negligible energy difference of 0.26 kJ mol⁻¹ between them. Azidoethene and azidomethanal both prefer the syn orientation of the azide group with respect to the C---C or C---O bonds, the computed energy difference between the anti and syn conformations being 3.31 and 30.3 kJ mol⁻¹ respectively.

The barrier to rotation around the C---N bond has been calculated to be 3.75 kJ mol⁻¹ in azidomethane while in azidoethane it was 3.30 and 9.40 kJ mol⁻¹ in the eclipsed anti-clinal (120°) and syn positions, respectively.

Complete harmonic force fields and dipole moment derivatives have been calculated for hydrazoic acid, azidomethane and for the two stable conformations of azidoethane. For azidoethane and azidomethanal only the azide part of the harmonic force field has been calculated. The theoretical harmonic force fields have been modified through scaling by a least squares refinement to the observed wavenumbers of hydrazoic acid, azidomethane and azidoethane (anti and gauche). Infrared vapour phase intensities have been calculated and theoretical spectra are presented for azidomethane and azidoethane.     

Semiempirical (AM1) and ab initio calculations of 2-X-adenine (X = H, F, Cl) and β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribofuranose

We performed semiempirical (AM1) and ab initio (3-21G and 4-31G^**) calculations, with complete optimization of geometry, for 2-X-adenine (X = H, F, Cl) and selected conformers of β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribo-furanose. Together (as 2-X-2',3'-didehydro-2',3'-dideoxyadenosine), or in separate conjunction with similar fragments, these structures belong to a group of 2',3'-dideoxynucleosides with potential anti-HIV activity.

The 2-X-adenine molecules are basically flat. For the halogenated species, especially the chlorine derivative, the results of the semiempirical method differ from the ab initio findings more widely than for adenine.

The results for the ribose derivative show the existence of conformers differing very little in energy. Ring puckering does not appear to depend on exocyclic torsion angles, structures with different conformations around the exocyclic C-C bond having similar ring conformations in all the cases analysed. The AMI method yielded geometries similar to those obtained ab initio with 3-21G.     

Proton-transfer and H2-elimination reactions of main-group hydrides EH4- (E = B, Al, Ga) with alcohols

The reaction of the isostructural anions of group 13 hydrides EH4- (E = B, Al, Ga) with proton donors of different strength (CH3OH, CF3CH2OH, and CF3OH) was studied with different theoretical methods [DFT/B3LYP and second-order M?ller-Plesset (MP2) using the 6-311++G(d,p) basis set]. The results show the general mechanism of the reaction: the dihydrogen-bonded (DHB) adduct (EH...HO) formation leads through the activation barrier to the next concerted step of H2 elimination and alkoxo product formation. The structures, interaction energies (calculated by different approaches including the energy decomposition analysis), vibrational E-H modes, and electron-density distributions were analyzed for all of the DHB adducts. The transition state (TS) is the dihydrogen complex stabilized by a hydrogen bond with the anion [EH3(eta2-H2)...OR-]. The single exception is the reaction of BH4- with CF3OH exhibiting two TSs separated by a shallow minimum of the BH3(eta2-H2)...OR- intermediate. The structures and energies of all of the species were calculated, leading to the establishment of the potential energy profiles for the reaction. A comparison is made with the mechanism of the proton-transfer reaction to transition-metal hydrides. The solvent influence on the stability of all of the species along the reaction pathway was accounted for by means of polarizable conductor calculation model calculations in tetrahydrofuran (THF). Although in THF the DHB intermediates, the TSs, and the products are destabilized with respect to the separated reactants, the energy barriers for the proton transfer are only slightly affected by the solvent. The dependence of the energies of the DHB complexes, TSs, and products as well as the energy barriers for the H2 release on the central atom and the proton donor strength is also discussed.     

Stereochemical studies of optically active 2-hydroxy-5-alkyl-δ-valerolactone derivatives as chiral dopant for ferroelectric liquid crystals

Both (2S, 5R)- and (2R, 5R)-2-hydroxy-5-alkyl-δ-valerolactone derivatives, cis and trans, respectively, show almost the same magnitude of spontaneous polarization (P_s) when added to a non-chiral smectic C mixture. The stereochemistry of these chiral dopants was studied using ¹H NMR. Trans derivatives seem to have a half-chair conformation with the 2, 5-diequatorial substituents and the cis derivatives have rather a flat conformation in solution. However in the liquid-crystalline phase, the cis and trans derivatives appear to change their conformation or the distribution of their conformations as the alkyl chain length is varied. The difference in the effect as a chiral dopant depends upon lateral interactions between chiral molecules through the solvent liquid crystal phase.     

Molecular determinants for drug-receptors : Part 11. The preferred conformation of N-(p-anisoyl)pyrrolidin-2-one (“Aniracetam”) in the solid and solution states as indicated by X-ray crystal structure analysis, dipole moment and theoretical calculations

N-(p-anisoyl)pyrrolidin-2-one in the crystalline state exhibites a cis—rans conrotatory conformation with N---CO and CO---C_ar rotational angles of 33.5° and 38.5° respectively, and the p-methoxy group situated cis to the central carbonyl bond, as shown by X-ray structure analysis. As suggested by dipole moment analysis and MMP2 molecular mechanics calculations, in solution similar conrotatory models hold for both c- and t-subconformers having the p-methoxy group cis or trans to the central carbonyl bond. INDO calculations were also carried out, indicating that both subconformers are equally stable.     

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.     

Determination of the chromophore structures in the photoinduced reaction cycle of phytochrome

The chromophore structures in the parent states Pr and Pfr as well as in the photocycle intermediate Lumi-R of oat phytochrome phyA are determined by comparison of the experimental resonance Raman spectra with calculated Raman spectra that have been obtained by density functional theory calculations (B3LYP) using scaled force fields. The spectra were calculated for various tetrapyrrole geometries including more than twenty different methine bridge isomers. For the parent states Pr and Pfr the best agreement in terms of vibrational frequencies, isotopic shifts, and Raman intensities was achieved with the ZZZasa and ZZEssa geometry, respectively. For the first intermediate Lumi-R, the chromophore geometry is concluded to be the ZZEasa configuration. These finding imply that the primary step of the photoactivation of phytochrome is the Z/E isomerization of the C-D methine bridge double bond, whereas the single bond remains in the anti conformation. The subsequent transition to the physiologically active state Pfr includes a (partial) single bond rotation of the A-B methine bridge.     

Cis- and trans-3-hexene: infrared spectrum in liquid argon solution, ab initio calculations of equilibrium geometry, normal coordinate analysis, and vibrational assignments

The infrared spectra of cis-3-hexene and trans-3-hexene dissolved in liquid argon have been obtained at temperatures from 93 to 120 K. The absorptions were observed with a low-temperature cell and a Fourier transform infrared spectrophotometer. Ab initio molecular orbital calculations were performed to obtain the equilibrium geometry, vibrational frequencies, force fields, and infrared intensities. The calculations were done at the Hartree-Fock level using 6-31G basis set. The Cartesian force fields from ab initio calculations have been converted to the force field in symmetry coordinates. The scale factors of ab initio calculated force fields were determined. Normal coordinate calculations were performed using a scaled quantum mechanical (SQM) force field. Vibrational normal modes calculated for the lowest energy rotamers of cis- and trans-3-hexene have been assigned to infrared absorption bands observed in liquid argon solution. The assignments were based on calculated frequencies and potential energy distributions. The equilibrium geometries of the two lowest energy rotamers (symmetry C₂ and C_s) of cis-3-hexene and of the three lowest energy rotamers (symmetry C_i, C₂, and C₁) of trans-3-hexene were calculated. Variable temperature studies of the infrared spectrum of cis- and trans-3-hexenes dissolved in liquid argon were done to obtain the ΔH of conversion between the rotamers C₂ and C_s of cis-3-hexene and between the rotamers C_i, C₂, and C₁ of trans-3-hexene.     

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.     

Diazocinones: synthesis and conformational analysis

1,2,4,5-Tetrazines (prepared from aryl nitriles) condense with isoxazolylcyclobutanones (prepared from 3-benzenesulfonyl-3-vinylcyclobutanol) in methanolic KOH to give conformationally restricted 6-isoxazol-5-yl-6,7-dihydro-5H-[1,2]diazocin-4-ones. The solution 1H NMR spectra of dihydrodiazocinone 1a with phenyl moieties at C3 and C8 reveal two conformations of the eight-membered heterocycle that are non-interconverting on the NMR time scale at ambient temperature. The kinetics of the conversion process, followed by 1H NMR between 21 and 70 degrees C in DMSO solution, yield an activation energy of approximately 21 kcal/mol relative to the kinetic conformer and show an equilibrated ratio of approximately 5:1 of the thermodynamic to the kinetic conformers. The electronic structure calculations on a model dihydrodiazocinone predict geometries for the two conformations. One of these geometries agrees with the X-ray crystallographic analysis of the thermodynamic conformation of 1a.     

Synthesis of dihydrodehydrodiconiferyl alcohol and derivatives through intramolecular C–H insertion

The natural dihydrobenzofuran neolignan 1 and its derivative 3 have been prepared through intramolecular C–H insertion catalyzed by a Rh(II) chiral complex. Moderate diastereo and enantioselectivities were observed. The cis and trans diastereomers were separated and unambiguously identified. The absolute configurations of the major isomers were established through chiral HPLC analysis and study of the Cotton effects in their circular dichroism curves.     

New mesomorphic organocyclosiloxanes I. Thermal behaviour and mesophase structure of organocyclotetrasiloxanes

cis-Cyclotetrasiloxanes of the formula cis-[PhSi(O)(OSiMe₂R)]₄ with R = Me, CH₂Cl, CH CH₂ and cis-[ClC₆H₄Si(O)(OSiMe₃)]₄ were synthesized and investigated in terms of their thermotropic phase transitions. Two ordered phases were observed for the cis-cyclotetrasiloxanes, one at lower temperature exhibiting the properties of a crystal and one at higher temperature exhibiting the properties of a plastically crystalline (3D) mesophase. A detailed examination of the mesophase behaviour and mesophase structure of octaphenylcyclotetrasiloxane was also carried out. It was shown that the thermal properties and structural characteristics of the mesophase are influenced by the structural characteristics of the substituent attached at the silicon atom in the tetracyclosiloxane. The new mesomorphic cis-cyclotetrasiloxanes are by far the largest molecules reported to date as forming plastic crystals, and the temperature region of the mesophase is much broader than in other plastic crystals. All five cyclotetrasiloxanes studied were found to be isomorphous in the 3D-mesophase and the low temperature forms of the two cis-cyclotetrasiloxanes: PhSi(O)(OSiMe₂R)₄ (R = Me, CH CH₂) were also isomorphous.     

Structural investigation of dibromobis(benzimidazole)Zn(II) complex

The molecular structure of the title complex [ZnBr₂(C₇H₆N₂)₂] was investigated by X-ray diffraction and IR spectroscopy methods. Molecules of zinc(II) complex crystallize in the triclinic crystal system with cell constants a=7.526(2) Å, b=7.8971(8) Å, c=13.431(1) Å, Z=2 and V=791.3(2) Å³. In the molecular structure, the Zn atom is coordinated tetrahedrally by two Br⁻ anions and two benzimidazole ligands. Intramolecular steric repulsions between Br⁻ anions and benzimidazole groups have been caused to cis configuration around the central metal atom.     

Structure and conformational stability of CH2CHCH2X (X=F, Cl and Br) molecules—post Hartree–Fock and density functional theory methods

The molecular structure and conformational stability of CH₂CHCH₂X (X=F, Cl and Br) molecules were studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 3-fluoropropene were optimized employing BLYP and B3LYP levels of theory of DFT method implementing 6-311+G(d,p) basis set. The MP2/6-31G^*, BLYP and B3LYP levels of theory of ab initio and DFT methods were used to optimize the 3-chloropropene and 3-bromopropene molecules. The structural and physical parameters of the molecules are discussed with the available experimental values. The rotational potential energy surface of the above molecules were obtained at MP2/6-31G^* and B3LYP/6-311+G(d,p) levels of theory. The Fourier decomposition of the rotational potentials were analyzed. The HF/6-31G^* and MP2/6-31G^* levels of theory have predicted the cis conformer as the minimum energy structure for 3-fluoropropene, which is in agreement with the experimental values, whereas the BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory reverses the order of conformation. The ΔE values calculated for 3-chloropropene at MP2/6-31G^*, BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory show that the gauche form is more stable than the cis form, which is in agreement with the experimental value. The same levels of theory have also predicted that the gauche form is stable than cis for 3-bromopropene molecule. The maximum hardness principle has been able to predict the stable conformer of 3-fluoropropene at HF/6-31G^* level of theory, but the same level of theory reverses the conformational stability of 3-chloropropene and 3-bromopropene molecules and MP2/6-31G^* level of theory predicted the stable conformer correctly.     

Intermolecular HH vibrations of dihydrogen bonded complexes H3EH(-)...HOR in the low-frequency region: theory and IR spectra

The results of DFT calculations of harmonic and anharmonic frequencies of the dihydrogen bonded (DHB) complexes H 3EH (-)...HOR (E = B, Al, Ga and HOR = CH 3OH, CF 3CH 2OH) in gas phase and in low polar medium (by CPCM model) in comparison with the partners are presented. Normal coordinate analysis of the low-frequency modes was carried out to assign the new vibrations induced by DHB formation by the potential energy distribution values. Among them, the intermolecular H...H stretching vibrations only have individual modes. The influence of central atom mass and isotope and the strength of the proton donor effects were determined. The systems convenient for IR studies were chosen from the calculation predictions. The spectral investigation was made on the BH 4 (-)/ROH complexes (ROH = CH 2FCH 2OH (MFE), CF 3CH 2OH (TFE), (CF 3) 2CHOH (HFIP)). The results of temperature dependence, isotope substitution, and influence of the proton-donor strength studies agree with the theoretical conclusions. Combination of experimental and theoretical approaches allowed determining for the first time the intermolecular stretching mode characterizing intrinsic DHB vibrations.     

气相中CrO2+和H2反应的理论研究

用密度泛函UB3LYP/6-311++G(3df, 3pdpd)//6-311G(2dd, p)方法计算研究了在二重态和四重态两个势能面上的气相反应：CrO₂⁺ + H₂→CrO⁺+ H₂O. 对影响反应机理和反应速率的势能面交叉进行了讨论, 并运用Hammond 假设和Yoshizawa 等的内禀反应坐标(IRC)单点垂直激发计算的方法找出了势能面交叉点(crossing point (CP)). 运用碎片分子轨道(fragment molecular orbital(FMO))理论, 对初始复合物2IM1和4IM1的轨道相关进行了分析, 解释了CrO₂⁺活化H—H σ键及H₂迁移的机理.     

The manifestation of non-bonded attraction in the physical properties of cis and trans olefins

Non-bonded attraction is suggested to account for a host of differences in the physical properties of cis and trans olefins of the type XHC=CHX. The main predictions are: (i) The cis isomer is more stable than the trans isomer; (ii) The C=C bond is longer and the C-X bonds are shorter for the cis isomer; (iii) The π MO's orbital energies of the two isomers differ such that the trans isomer is a better electron donor and electron acceptor than the cis isomer. Ab initio calculations at the STO-3G and the 4-31G levels in support of the model are presented. The photoelectron spectra of cis and trans difluoro, dichloro and dibromoethylene are discussed, and found to be in accord with our qualitative model.     

Vibrational spectra of some tetraalkylammonium acid salts of acetic acids. Hydrogen bonding in solids and solutions

Infrared and Raman spectra are reported of several hydrogen dicarboxylates of the composition MH(D)X₂ (M = tetramethyl or tetrabutylammonium, X = CH₃COO, CF₃COO, CCl₃COO) as solids and solutions in nonaqueous solvents. It is shown that very strong hydrogen bonding persists in solution although in some cases the high symmetry observed in the solid is lost by dissolution of melting. The hydrogen diacetate anion appears to have different conformations in the solid and solution. Calculations in the ab-initio scheme (STO-3G) for the trans and cis forms of this ion, without and with countercharges, demonstrate that the cis conformation is more stable in the latter case whereas the trans conformation is preferred without charges.