First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers

First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi=psi=anti) orientation corresponding to approximately the betaL backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans-->cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.     

Folded and unfolded conformations of the omega-3 polyunsaturated fatty acid family: ch(3)ch(2)[ch=chch(2)](b)[ch(2)](m)cooh: first principles study

Polyunsaturated fatty acids (PUFA) like stearidonic acid (SDA;18:4 n-3) eicosapentaenoic acid (EPA; 20:5 n-3), and docosahexaenoic acid (DHA; 22:6 n-3) and its chain fragment models were studied at B3LYP/6-31G(d) levels of theory. Significant conformations for the cis and trans isomers were selected to obtained the thermodynamic functions (DeltaH, DeltaS, DeltaG) for the cis-trans isomerization and for folding using the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) level of theory. The structural analysis shows that there are significant differences in thermodynamic function of the trans- and cis-PUFAs. The trans-cis isomerization energy values reinforce the consistency and the relative accuracy of theoretical model calculations. The observed flexibility of naturally cis PUFAs could be explained by a very special "smooth basin" PES of the motif of sp(2)-sp(3)-sp(2) hybrid states as reported previously (J. Phys. Chem. A 2005, 109, 520-533). We assumed that intrinsic thermodynamic functions may describe this flexible folding process. The folding enthalpy as well as the folding entropy suggests that there is a new role of the cis-PUFAs in membranes: these cis isomers may have a strong influence on membrane stability and permeability. The average length of the cis helix and beta PUFA was approximated. The difference between the lengths of these two structures is approximately 10 A.     

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.     

Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy

Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.     

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

Ab initio study of the structures and stabilities of the dimer of ethyl cation, (C(2)H(+)(5))(2) and related C(4)H(10)(2+) isomers.

Ab initio calculations at the MP4(SDTQ)/6-311G//MP2/6-31G level were performed to study the structures and stabilities of the dimer of ethyl cation, (C(2)H(+)(5))(2), and related C(4)H(10)(2+) isomers. Two doubly hydrogen bridged diborane type trans 1 and cis 2 isomers were located as minima. The trans isomer was found to be more favorable than cis isomer by only 0.6 kcal/mol. Several other minima for C(4)H(10)(2+) were also located. However, the global energy minimum corresponds to C-H (C(4) position) protonated 2-butyl cation 10. Structure 10 was computed to be substantially more stable than 1 by 31.7 kcal/mol. The structure 10 was found to be lower in energy than 2-butyl cation 13 by 34.4 kcal/mol.     

Theoretical Study of Halogen Effect in Isomerization of 2-Halo-[9]-annulen Anion at the DFT Level

Cis-trans isomerization of [9]-annulenanion(1) and its 2-fluoro-,2-chloro-and 2-bromo-derivatives(2,3 and 4,respectively) were investigated at the HF/6-31G* and B3LYP/6-311++G** levels of theory.Cis,cis,cis,cis structures appear more stable than their corresponding cis,cis,cis,trans-isomers.The relative height of energy barriers for cis-trans isomerization is:2cis > 1cis > 3cis > 4cis.This trend for the reverse trans-cis isomerization follows the electronegativity of the substituent at C-2(2trans > 3trans > 4trans > 1trans).     

周边含己氧基的三代光致变色液晶树枝状大分子的光化学

报道了新化合物含108个己氧基端基的三代(G3)碳硅烷光致变色液晶树状大分子在溶液中的反-顺光异构化反应速率常数k_p, 光回复异构化正/逆反应速率常数k_t和k_c, 热回复异构化反应速率常数k_H, 光回复异构化反应平衡常数k_t/k_c, 活化能E, 异构转化率A/A₀及组分比A'/A₀. G3的光致变色反应速率常数的数量级为10^－1 s^－1, 而侧链含偶氮基元的光致变色聚硅氧烷的光致变色反应速率常数的数量级为10^－8 s^－1, 因此G3的光响应速率比后者快10⁷倍.     

Synthesis of heteroaryl imines: theoretical and experimental approach to the determination of the configuration of C=N double bond

The reaction between an iminophosphorane with furan-2-carbaldehyde, thiophene-2-carbaldehyde, furan-3-carbaldehyde, and thiophene-3-carbaldehyde at 60 degrees C gives the corresponding trans imines in 53-84% yields, while the same reaction at 100 degrees C gives a mixture of the corresponding trans and cis imines. Whether the iminophosphorane reacted with 5-nitrofuran-2-carbaldehyde or 5-nitrothiophene-2-carbaldehyde only the trans imines were obtained in 85-89% yields. The irradiation of the imines obtained from thiophene-2-carbaldehyde and thiophene-3-carbaldehyde gave the corresponding photocyclization products. Cis/trans stereochemistry of the imines can be assigned simulating the UV-vis spectra. In the case of the imine from furan-2-carbaldehyde the computed spectra are characterized by an intense absorption at 361 and 357 nm respectively for the trans-1 and trans-2 structures. No other absorptions of comparable intensity have been predicted: the agreement with the experimental spectrum can be considered good. Furthermore, the experimental weak peaks at 280 and 270 nm can be associated to the computed transitions at 278 and 260 nm for the trans-1 isomer. Several minima of the energy surface can be assigned to the cis isomer, and they all present a very similar energy. The structures of the cis-1 and cis-2 isomers present quite coincident computed electronic spectra. In both cases, the computed spectrum shows two principal features. For the cis-1 structure, the first characteristic absorption is located at 414 nm and the second one at 284 nm. For the cis-2 structure, the first feature is located at 412 nm and the second one at 286 nm. The second transition is computed somewhat more intense. The experimental spectrum could be the consequence of similar populations of the planar cis structure (cis-3) and nonplanar cis structures (cis-1, cis-2, and their enantiomers).     

Effects of molecular structure on the stability of a thermotropic liquid crystal. Gas electron diffraction study of the molecular structure of phenyl benzoate.

As a model of the core of molecules forming liquid crystals, the molecular structure of phenyl benzoate (Ph-C(=O)-O-Ph) at 409 K was determined by gas electron diffraction, and the relationship between the gas-phase structures of model compounds and the nematic-to-liquid transition temperatures was studied. Structural constraints were obtained from RHF/6-31G ab initio calculations. Vibrational mean amplitudes and shrinkage corrections were calculated from the harmonic force constants given by normal coordinate analysis. Thermal vibrations were treated as small-amplitude motions, except for the phenyl torsion, which was treated as a large-amplitude motion. The potential function for torsion was assumed to be V(phi(1),phi(2)) = V(12)(1 - cos 2phi(1))/2 + V(14)(1 - cos 4phi(1))/2 + V(22)(1 - cos 2phi(2))/2, where phi(1) and phi(2) denote the torsional angles around the C-Ph and O-Ph bonds, respectively. The potential constants (V(ij)()/kcal mol(-)(1)) and the principal structure parameters (r(g)/A, angle(alpha)/deg) with the estimated limits of error (3sigma) are as follows: V(12) = -1.3 (assumed); V(14) = -0.5(9); V(22) = 3.5(15); r(C=O) = 1.208(4); r(C(=O)-O) = 1.362(6); r(C(=O)-O) - r(O-C) = -0.044 (assumed); r(C(=O)-C) = 1.478(10); = 1.396(1); angleOCO = 124.2(13); angleO=CC = 127.3(12); angleCOC = 121.4(22); ( angleOCC(cis) - angleOCC(trans))/2 = 3.0(15); ( angleC(=O)CC(cis) - angleC(=O)CC(trans))/2 = 4.8(17), where < > means an average value and C-C(cis) and C-C(trans) bonds are cis and trans to the C(=O)-O bond, respectively. The torsional angle around the O-Ph bond was determined to be 64(+26,-12) degrees. An apparent correlation was found between the contributions of the cores to the clearing point of liquid crystals and the gas-phase structures of model compounds of the cores of mesogens, i.e., phenyl benzoate, trans-azobenzene (t-AB), N-benzylideneaniline, N-benzylideneaniline N-oxide (NBANO), trans-azoxybenzene (t-AXB), and trans-stilbene. The structures of t-AB, NBANO, and t-AXB have been obtained by our research group.     

Counter-current chromatographic estimation of hydrophobicity of Z-(cis) and E-(trans) enalapril and kinetics of cis/trans isomerization

The kinetics of Z-(cis)/E-(trans) isomerization of enalapril was investigated by reversed phase high-performance liquid chromatography (RP-HPLC) using a monolith ODS column under a series of different temperature and pH conditions. At a neutral pH 7, the rate (k(obs)) of Z-(cis)/E-(trans) isomerization of enalapril at 4 degrees C (9.4 x 10(-3)min(-1)) is much lower than at 23 degrees C (1.8 x 10(-1)min(-1)), while the fractional concentration of Z-(cis) isomer is always higher than that of E-(trans) isomer in the pH range 2-7. The fractional concentration of the E-(trans) isomer becomes a maximum (about 40%) in the pH range 3-6, where enalapril exists as a zwitterion. The hydrophobicity (logP(O/W)) of both isomers was estimated by high-speed counter-current chromatography (HSCCC). Normal phase HSCCC separation using a tert-butyl methyl ether-acetonitrile-20mM potassium phosphate buffer (pH 5) two-phase solvent system (2:2:3, v/v/v) at 4 degrees C was effective in partially separating the isomers, and the partition coefficient (K) of each isomer was directly calculated from the retention volume (V(R)). The logP(O/W) values of Z-(cis) and E-(trans) isomers were -0.46 and -0.65, respectively.     

Photophysical studies of the trans to cis isomerization of the push-pull molecule: 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.     

Selection of the cis and trans phosph(III)azane macrocycles [{P(mu-NtBu)}2(1-Y-2-NH-C6H4)]2(Y=O, S)

The 1 : 1 reactions of [ClP(mu-NtBu)]2 with the difunctional aromatic amines 1,2-1-YH-2-NH2-C6H4 in the presence of Et3N give the dimeric phosph(III)azane macrocycles [{P(mu-NtBu)2(1-Y-2-HN-C6H4)]2, predominantly as the cis isomer in the case of Y=O (1.cis) and as the trans isomer for Y=S (2.trans). Model M.O. calculations suggest that the selection of the cis and trans isomers is not thermodynamically controlled. The alternative isomers 1.trans and 2.cis are generated exclusively by the deprotonation of the model intermediates [(1-Y-2-NH2-C6H4)P(mu-NtBu)]2[Y=O (3), S (4)] with nBuLi followed by cyclisation with [ClP(mu-NtBu)]2. The solid-state structures of 1.cis/trans(50 : 50), 2.cis, 3 and 4 are reported.     

Theoretical study of the mechanism of NO2 production from NO + ClO

The reaction of NO with ClO has been studied theoretically using density-functional and wave function methods (B3LYP and CCSD(T)). Although a barrier for cis and trans additions could be located at the RCCSD(T) and UCCSD(T) levels, no barrier exists at the B3LYP/6-311+G(d) level. Variational transition state theory on a CASPT2(12,12)/ANO-L//B3LYP/6-311+G(d) surface was used to calculate the rate constants for addition. The rate constant for cis addition was faster than that for trans addition (cis:trans 1:0.76 at 298 K). The rate constant data summed for cis and trans addition in the range 200-1000 K were fit to a temperature-dependent rate in the form kdi) = 3.30 x 10(-13)T(0.558) exp(305/T) cm3.molecule(-1).s(-1), which is in good agreement with experiment. When the data are fit to an Arrhenius plot in the range 200-400 K, an activation barrier of -0.35 kcal/mol is obtained. The formation of ClNO2 from ONOCl has a much higher activation enthalpy from the trans isomer compared to the cis isomer. In fact, the preferred decomposition pathway from trans-ONOCl to NO2 + Cl is predicted to go through the cis-ONOCl intermediate. The trans --> cis isomerization rate constant is kiso = 1.92 x 10(13) exp(-4730/T) s(-1) using transition state theory.     

Donor atom dependent geometric isomers in mononuclear oxo-molybdenum(V) complexes: implications for coordinated endogenous ligation in molybdoenzymes

We have previously demonstrated that the complex [(L1O)MoOCl(2)], where L1OH = (2-hydroxy-3-tert-butyl-5-methylphenyl)bis(3,5-dimethylpyrazolyl)methane, exists as both cis and trans isomers (Kail, B.; Nemykin, V. N.; Davie, S. R.; Carrano, C. J.; Hammes, B. S.; Basu, P. Inorg. Chem. 2002, 41, 1281-1291). Here, the cis isomer is defined as the geometry with the heteroatom in the equatorial position, and the trans isomer is designated as the geometry with the heteroatom positioned trans to the terminal oxo group. The trans isomer represents the thermodynamically more stable geometry as indicated by its spontaneous formation from the cis isomer. In this report, we show that for complexes of [(LO)MoOCl(2)], where LOH is the sterically less restrictive (2-hydroxyphenyl)bis(3,5-dimethylpyrazolyl)methane, only the trans isomer could be isolated, while in the corresponding thiolate containing ligand (2-dimethylethanethiol)bis(3,5-dimethylpyrazolyl)methane (L3SH) only the cis isomer could be observed. In addition, we have isolated and structurally characterized the complex [(L1O)MoO(OPh)(Cl)], a rare example of a species possessing both cis and trans phenolates. Using DFT calculations, we have investigated the origins of the differences in stability between the cis and trans isomers in these complexes and suggest that they are related to the trans influence of the oxo-group. Crystal data for [(LO)MoOCl(2)] (1) include that it crystallizes in the triclinic space group P(-)1 with cell dimensions a = 8.9607 (12) A, b = 10.596 (4) A, c = 13.2998 (13) A, alpha = 98.03 (2) degrees, beta = 103.21 (2) degrees, gamma = 110.05(2) degrees, and Z = 2. [(L1O)MoO(OPh)Cl].2CH(2)Cl(2) (2.2CH(2)Cl(2)) crystallizes in the triclinic space group P(-)1 with cell dimensions a = 12.2740 (5) A, b = 13.0403 (5) A, c = 13.6141 (6) A, alpha = 65.799 (2) degrees, beta = 64.487 (2) degrees, gamma = 65.750 (2) degrees, and Z = 2. [(L3S)Mo(O)Cl(2)] (3) crystallizes in the orthorhombic space group Pna2(1), with cell dimensions a = 13.2213 (13) A, b = 8.817 (2) A, c = 15.649 (4) A, and Z = 4. The implications of these results on the function of mononuclear molybdoenzymes such as sulfite oxidase, and the DMSO reductase, are discussed.     

Trans or (Unusual) Cis Geometry in d(2) Octahedral Dioxo Complexes. A DFT Study

Geometry optimization of the cis and the trans isomers of several octahedral dioxo complexes of d(2) electronic configuration are performed using the gradient-corrected density functional theory (B3LYP and, for some key structures, BP86). With only monodentate sigma donor ligands (ReO(2)(NH(3))(4)(+), 7), the usual energy order is found (i.e., the trans isomer is the most stable). Complexes with a chelating bidentate ligand, OsO(2)(OCH(2)CH(2)O)(NH(3))(2) (10) and ReO(2)(HN=CHCH=NH)(NH(3))(2)(+) (11), are used as models for the experimental complexes 5 and 2 in which the arrangement of the O=M=O unit is trans and cis, respectively. Our calculations actually show an inversion of the relative energy of the two isomers in going from 10 to 11: while the trans isomer is found to be the most stable in 10, the unusual cis diamagnetic isomer is favored by about 29 kcal mol(-)(1) in 11. This result is traced to the geometric and electronic properties of the bidentate ligand, in particular an acute bite angle and good pi acceptor character. In complex 14 with a bipyridine chelating ligand (weaker pi acceptor than diaza-1,4-butadiene in 11), this energy difference is, however, reduced to 7.5 kcal mol(-)(1) (partial geometry optimization).     

Kinetics of the cis,cis to trans,trans isomerization of 1,1,2,2,5,5,6,6-octamethyl-1,2,5,6-tetrasilacycloocta-3,7-diene

The kinetics of the ruthenium-promoted cis,cis to trans,trans isomerization of 1,1,2,2,5,5,6,6-octamethyl-1,2,5,6-tetrasilacycloocta-3,7-diene were investigated. Incubation of a ruthenium alkylidene complex, (Cy(3)P)RuCl(2)(==CHPh)Ru(p-cymene)Cl(2), in CD(2)Cl(2) for 5 days at 40 degrees C afforded a catalytically active ruthenium species that was shown to be responsible for promoting the isomerization. The isomerization was observed to proceed in two steps: (1) conversion of the starting cis,cis isomer to a proposed cis,trans intermediate and (2) subsequent conversion of the intermediate to the product trans,trans isomer. Kinetic studies demonstrated that the two steps are first-order with respect to the concentrations of the cis,cis isomer, the intermediate, and the ruthenium alkylidene complex. The data were further consistent with a mechanism involving bimolecular hydride addition-elimination during the two isomerization steps.     

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.     

All-cis helical polypeptides

The possibility of all-cis open-chain polypeptides is rarely addressed, owing to three main reasons, namely, (i) the extreme scarcity of cis peptide bonds in naturally occurring proteins and peptides, (ii) the lesser thermodynamic stability (by about 2.5 kcal/mol) of cis amide bonds with respect to their trans counterparts, and (iii) widely held preconceptions about the so-called "steric clash" between lateral chains borne by two successive alpha carbons. Quantum-chemistry calculations performed on alanine tridecamers show how the latter constraints can be efficiently relieved through proper phi/psi adjustments along the backbone, leading to several helical arrangements--presumably the only permitted regular structures. Four more-or-less regular helices were thus characterized, one of them, a superhelix, exhibiting intramolecular hydrogen bonds. Understanding and anticipating all-cis open-chain structures not only make use of the classical Ramachandran maps at each C alpha i, relating to E = f(phi i,psi i), but also require the profile of a new kind of conformational dependence, the plaque maps, relating to E = f(phi i,psi i-1). The obvious coupling between two such maps enforces conformational dependence between two consecutive C alpha's, somewhat questioning in this context the customary "local effects", and presumably reducing the whole chain plasticity. Whereas cis thermodynamic penalty cannot be abolished locally, energy clues indicate that assembling cis-prepared building units is an exothermic process. Besides, once built up, the all-cis backbone should be difficult to unlock, thus affording reasonable kinetic stability.     

1.1](3,3')-azobenzenophane: novel crystal structure and cis-trans isomerization of distorted azobenzene

[formula: see text] [1.1](3,3')-Azobenzenophane, in which two azobenzenes are cyclically connected by -CH2- chains at the meta positions, has been synthesized. The crystal structures of all isomers have been revealed. This is the first report on the crystal structure of the cis isomer of macrocyclic azobenzenes. The trans,trans isomer was slightly distorted, the trans,cis isomer highly deformed, and the cis,cis isomer unstrained. The thermal stability of cis isomers in solutions are deducible from the crystal structures.