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.     

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.     

Multiple steps and multiple excitations in photoisomerization of azobenzene

Detailed understanding of femtosecond-scale photochemical processes requires dynamical simulations that are complementary to interpretations based on transitions between energy surfaces. For cis to trans photoisomerization of azobenzene following a 100 fs laser pulse, we find that the mechanism is rotation about the central NN bond, and the process is complete in less than 1 ps. The initial excitation and subsequent de-excitation are each achieved via multiple steps, with the molecule always in a superposition of electronic states, as the 3N nuclear degrees of freedom are excited by the laser pulse.     

Photochemical reaction kinetics in optically dense media: The influence of thermal reactions

The kinetics of photochemical reactions in optically dense media essentially free from diffusion was considered. The photochromic isomerization A ↔ B was studied as an example. If thermal isomerization is possible, a stationary state is achieved in time determined by rate constants for the thermal reactions. The concentration wave profile is changed during the photochemical reaction propagation. Low values of thermal reaction constants and decrease in sample optical density during photochemical isomerization were found to be essential for maximal wave penetration into the sample. Sharp concentration gradients of A and B can be observed when both the optical density is increased during photochemical isomerization and the quantum yield of the direct photochemical reaction A → B is higher than that of the reverse photochemical reaction B → A.     

Interaction between naphthyl-indolyl-ethenes and aliphatic amines: Effects on fluorescence and trans→cis photoisomerization

The fluorescence of two trans naphthyl-indolyl-ethenes in solvents of different polarity and H-bonding ability is quenched by aliphatic amines. The H-bonded complexes formed both in the ground- and in the first excited singlet state are responsible for the quenching in non-hydroxylated media. In methanol the interaction, which occurs only in the excited state, leads to the deprotonation of the indolyl-moiety. The consequences of the quenching on the trans→cis photoisomerization yield are reported.     

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.     

Syntheses, crystal structures and electronic properties of a series of copper(II) complexes with 3,5-halogen-substituted Schiff base ligands and their solutions

We have systematically investigated the structural features, electronic properties, thermally-induced structural phase transitions and absorption spectra depending on the solvent for ten Cu(II) complexes with 3,5-halogen-substituted Schiff base ligands. Structural characterization of two new complexes, bis(N-R-1-phenylethyl- and N-R,S-2-butyl-5-bromosalicydenaminato-κ²N,O)copper(II), reveals that they afford a compressed tetrahedral trans-[CuN₂O₂] coordination geometry with trans-N–Cu–N = 159.4(2)° and trans-O–Cu–O = 151.7(3)° for the 1-phenylethyl complex and trans-N–Cu–N = 157.9(3)° and trans-O–Cu–O = 151.0(3)° for the 2-butyl one. All the complexes exhibit a structural phase transition by heating in the solid state regardless of their structures at room temperature. The absorption spectra of a series of ten complexes exhibit a slight shift of the d–d band at 16 000–20 000 cm⁻¹ and remarkable shift of the π–π* band at 24 000–28 000 cm⁻¹, which suggests that the dipole moment of the solvents presumably affects the conformation of the π-conjugated moieties of the ligands rather than the coordination environment. We have also attempted ‘photochromic solute-induced solvatochromism’ by a system of bis(N-R-1-phenylethyl-3,5-dichlorosalicydenaminato-κ²N,O)copper(II) and photochromic 4-hydroxyazobenzene in chloroform solution. We successfully observed a change of the d–d and π–π* bands of the complex in the absorption spectra caused by cis–trans photoisomerization of 4-hydroxyazobenzene.     

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.     

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.     

Ideal gas state thermodynamic functions for a series of halogenated propenes

The thermodynamic functions, C√_p, S√,—F√_o—H√)/T and (H√—H√_o)/T have been calculated in the ideal gas state at one atmosphere for the following halogenated propenes: cis-1-chloropropene; trans-1-chloropropene; cis-1-bromopropene; trans-1-bromopropene; 2-fluoropropene; 2-chloropropene; 2-bromopropene; 2-iodopropene; cis-3-fluoropropene; gauche-3-fluoropropene; isomeric-3-fluoropropene; mixture; cis-3-chloropropene; gauche-3-chloropropene; isomeric-2-chloropropene mixture; cis-3-bromopropene; gauche-3-bromopropene; isomeric-3-bromopropene; mixture; cis-3-iodopropene; gauche-3-iodopropene and isomeric-3-iodopropene mixture. The agreement with other results, whenever available, is very good.     

Molecular orientation of azobenzene chromophores in ultrathin polymer nanosheets studied by attenuated total reflection spectroscopy

This paper describes characterization of molecular orientation for azobenzene moieties in a polymer nanosheet. Copolymers of N-[4-(phenylazo)phenyl] acrylamide (PAZoA) with tert-pentyl acrylamide (tPA) were synthesized and the monolayers deposited on tapered quartz waveguides by Langmuir–Blodgett (LB) technique. Spectroscopic properties of the copolymer (p(tPA/PAZoA)) monolayers were monitored by integrated optical waveguide technique on the molecular level. Molecular orientation of the azobenzene was precisely determined by polarized absorption spectra. It was found that the azobenzene groups took a horizontal orientation and distributed uniformly in the p(tPA/PAZoA) monolayer without significant PAZoA aggregation. Photoisomerization process from trans to cis form was also investigated. More than half of the trans form (60–70%) was photoisomerized under unpolarized light irradiation, and the photoisomerization rate was independent on the PAZoA contents. This implies that the microenvironment of PAZoA moieties was almost the same in three different p(tPA/PAZoA) monolayers.     

An infrared spectroscopic study of photo-induced reorientation in dye containing liquid-crystalline polymers

Infrared spectroscopy is used to study simultaneously the orientational behaviour of different segments of dye containing liquid-crystalline side group copolymers in sandwich type films of about 2 μm thickness. Under continuous irradiation with polarized light above and below T_g of the polymers both azobenzene and phenyl benzoate side groups reorient preferentially normal to the film plane leading to a strongly biaxial orientation distribution. The analysis of the kinetics reveals that the reorientation is essentially a mono-exponential process with an additional faster process only found for the azobenzene dye and assigned to the initial trans to cis isomerization step. Investigation of an isotropic copolymer system containing azobenzene in the side groups shows that an anisotropy can be induced through irradiation with polarized light that is strongly dependent on temperature.     

Interaction of sodium cholate with dioctadecyldimethylammonium chloride vesicles in aqueous dispersion

Mixtures of dioctadecyldimethylammonium chloride (DODAC) cationic vesicle dispersions with aqueous micelle solutions of the anionic sodium cholate (NaC) were investigated by differential scanning calorimetry, DSC, turbidity and light scattering. Within the concentration range investigated (constant 1.0 mM DODAC and varying NaC concentration up to 4 mM), vesicle → micelle → aggregate transitions were observed. The turbidity of DODAC/NaC/water depends on time and NaC/DODAB molar concentration ratio R. At equilibrium, turbidity initially decreases smoothly with R to a low value (owing to the vesicle–micelle transition) when R = 0.5–0.8 and then increases steeply to a high value (owing to the micelle–aggregate transition) when R = 0.9–1.0. DSC thermograms exhibit a single and sharp endothermic peak at T_m ≈ 49 °C, characteristic of the melting temperature of neat DODAC vesicles in water. Upon addition of NaC, T_m initially decreases to vanish around R = 0.5, and the main transition peak broadens as R increases. For R > 1.0 two new (endo- and exothermic) peaks appear at lower temperatures indicating the formation of large aggregates since the dispersion is turbid. All samples are non-birefringent. Dynamic light scattering (DLS) data indicate that both DODAC and DODAC/NaC dispersions are highly polydisperse, and that the mean size of the aggregates tends to decrease as R increases.     

Time resolved spectroscopy on Pigment Yellow 101 in solid state

The photochemistry of the fluorescent Pigment Yellow 101 (P.Y.101) in the crystalline phase is investigated combining time resolved vibrational and electronic spectroscopy. The experiments reveal a complex reaction dynamics spanning several orders of magnitude in time and including excited state intramolecular proton transfer (ESIPT) from the initial trans-diol conformer. Following photoexcitation and the subsequent wavepacket motion out of the Franck–Condon region two tautomers, an excited trans-diol and trans-keto state are formed. The cis–trans isomerization of the keto form, which was experimentally observed and theoretically confirmed in DFT calculations in studies on P.Y.101 in solution is obstructed in the solid state, consequently the formation of the cis conformer is not directly observed. In addition, a long lived photoproduct with red shifted vibrational frequencies is identified. The life time of this intermediate is determined to be 50 μs, although an unambiguous assignment to a specific molecular configuration cannot be given at present.     

The active catalytic species and its isomerisation in the catalytic carbonylation of methanol — a density functional study

The Monsanto acetic acid process is one of the most effective ways to produce acetic acid industrially. This process has been studied experimentally but theoretical investigations are so far sparse. In the current work the active catalytic species [Rh(CO)₂I₂]⁻ (1) and its isomerisation has been studied theoretically using the hybrid B3LYP exchange and correlation functional. Similar calculations has been performed for the iridium complex [Ir(CO)₂I₂]⁻ (2) that also is catalytically active in the methanol carbonylation. Experimental work has confirmed the existence of the cis forms of the active catalytic species, but they do not rule out the possibility of the trans isomers. Our gas phase results show that cis-1 has 4.95 kcal/mol lower free energy than trans-1, and cis-2 has 10.39 kcal/mol lower free energy than trans-2. In the case of rhodium, trans-1 can take part to the catalytic cycle but in case of iridium this is not very likely. We have also investigated the possible mechanisms of the cis to trans conversions. The ligand association mechanism gave free energy barrier of 13.7 kcal/mol for the rhodium complex and 19.8 kcal/mol for iridium. Thus the conversion for the rhodium complex is feasible whereas for iridium it is unlikely.     

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.     

Infrared and Raman spectra, conformational stability, ab initio calculations, and vibrational assignments for methylaminothiophosphoryl difluoride

Infrared spectra (4000–50 cm⁻¹) of the vapor, amorphous and crystalline solids and Raman spectra (3600–10 cm⁻¹) of the liquid with qualitative depolarization data as well as the amorphous and crystalline solids of methylaminothiophosphoryl difluoride, CH₃N(H)P(=S)F₂, and three deuterated species, CD₃N(H)P(=S)F₂, CH₃N(D)P(=S)F₂, and CD₃N(D)P(=S)F₂, have been recorded. The spectra indicate that in the vapor, liquid and amorphous solid a small amount of a second conformer is present, whereas only one conformer remains in the low temperature crystalline phase. The near-infrared spectra of the vapor confirms the existence of two conformers in the gas phase. Asymmetric top contour simulation of the vapor shows that the trans conformer is the predominant vapor phase conformer. From a temperature study of the Raman spectrum of the liquid the enthalpy difference between the trans and near-cis conformers was determined to be 368±15 cm⁻¹ (4.41±0.2 kJ/mol), with the trans conformer being thermodynamically preferred. Ab Initio calculations with structure optimization using the 6-31G(d) and 6-311+G(d,p) basis sets at the restricted Hartree–Fock (RHF) and/or with full electron correlation by the perturbation method to second order (MP2) support the occurrence of near-trans (5° from trans) and near-cis (20° from cis) conformers. From the RHF/6-31G(d) calculation the near-trans conformer is predicted to be the more stable form by 451 cm⁻¹ (5.35 kJ/mol) and from the MP2/6-311+G(d,p) calculation by 387 cm⁻¹ (4.63 kJ/mol). All of the normal modes of the near-trans rotamer have been assigned based on infrared band contours, depolarization values and group frequencies and the assignment is supported by the normal coordinate calculation utilizing harmonic force constants from the MP2/6-31G(d) ab initio calculations.     

Utilization of Azobenzene Units to Control Zinc-mediated Ring Opening Polymerization of Cyclic Esters

Salicylaldimine Zn(Ⅱ) complexes bearing azobenzene moieties were prepared to catalyze ring opening polymerization of various cyclic esters. The different reactivities of the trans and cis isomers of the zinc complexes provide a facile strategy to control polymerization processes as well as the compositions of the resultant polymers.     

Determination of cilnidipine, a new calcium antagonist, in human plasma using high performance liquid chromatography with tandem mass spectrometric detection

A rapid, sensitive and reliable high performance liquid chromatographic method coupled with tandem mass spectrometry (HPLC–MS/MS) has been developed and validated for the determination of cilnidipine, a relatively new calcium antagonist, in human plasma. The reversed-phase chromatographic system was interfaced with a TurboIonSpray (TIS) source. Nimodipine was employed as the internal standard (IS). Sample extracts following protein precipitation were injected into the HPLC–MS/MS system. The analyte and IS were eluted isocratically on a C18 column, with a mobile phase consisting of CH₃OH and NH₄Ac (96:4, v/v). The ions were detected by a triple quadrupole mass spectrometric detector in the negative mode. Quantification was performed using multiple reaction monitoring (MRM) of the transitions m/z 491.2 → 122.1 and m/z 417.1 → 122.1 for cilnidipine and for the IS, respectively. The analysis time for each run was 3.0 min. The calibration curve fitted well over the concentration range of 0.1–10 ng mL⁻¹, with the regression equation Y = (0.103 ± 0.002)X + (0.014 ± 0.003) (n = 5), r = 0.9994. The intra-day and inter-day R.S.D.% were less than 12.51% at all concentration levels within the calibration range. The recoveries were between 92.71% and 97.64%. The long-term stability and freeze-thaw stability were satisfying at each level. The present method provides a modern, rapid and robust tool for pharmacokinetic studies of cilnidipine.     

Refined heat capacity of LaPO4 in the temperature range 0–1600 K

In the present work temperature dependence of heat capacity of cesium tantalum tungsten oxide has been measured first in the range from 7 to 350 K and then between 330 and 630 K, respectively, by precision adiabatic vacuum and dynamic calorimetry. The experimental data were used to calculate standard thermodynamic functions, namely the heat capacity C_p° (T), enthalpy H°(T) − H°(0), entropy S°(T) − S°(0) and Gibbs function G°(T) − H°(0), for the range from T → 0 to 630 K. The structure of CsTaWO₆ is refined by the Rietveld method: space group F d3m, Z = 8, a = 10.3793(2) Å, V = 1118.14(4) Å³. The high-temperature X-ray diffraction was used for the determination of temperature of phase transition and coefficient of thermal expansion.