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An examination of the mechanism of thermally induced rearrangement of 7-(trans-butenylidine)bicyclo(4.1.0)heptane to 8-methylbicyclo-(5.3.0)undeca-1(2),9-diene revealed opposite stereospecificity to that predicted by orbital symmetry conservation. The experiment showed the involvement of achiral transition states and intermediates. Minima and transition states were calculated by a HONDO program using a complete active space wave function with a configuration of six electrons and six optimized orbits that would make and break bonds. Starting material was recovered unchanged after formation of racemic product by pyrolysis.

The superoxide-mediated oxidation of tetraphenylcyclopentadiene leads to a variety of products and trace amount of tetracyclone. The first step of reaction is deprotonation. The carbanion formation is followed by a set of autoxidative processes. These consist of oxygenation, dehydration or peroxy anion cyclization and oxidative cleavage. In the equilibrium mix of 2-ene-1,5-diones the cis isomer is the dominant product because of electronic and steric effects.

Arg82 was replaced with Lys to analyse the role of Arg82 in the catalysis of proton transfer in bacteriorhodopsin, which has an intrinsic pK(sub a) of about 1.7 pH units lower than that of Arg. From the R82K mutant expressed in Halobacterium salinarium, it was found that the pK(sub a) of purple-to-blue transition at low temperature is about 3.6. At high pH in the blue-to-purple transition, the pK(sub a) was 8.0, the rate constant of dark adaption, k(sub da), is proportional to the fraction of blue membrane between pH = 2 and 10, and the efficiency of protein transfer in R82K under steady state is at least 40%.

The copolymerization of carbon monoxide and alkene on a palladium (II) center follows a stepwise and stereoregular insertion reaction pathway, and the product stability is dependent on the nature of the anions present in the complex. The equilibrium of the reaction is directed by the nature of the alkene, solvent and by the anion. Powerful coordinating anions stabilize the acetylpalladium (II) oligomers while the strained alkenes are copolymerized if the reaction conditions are optimized.

A transition intermediate state of the form pentamethylenepropane (PMP) is obtained by the isomerization of the 2,4-dibenzylidene-bicyclo(3.1.0)hexan- 3-one at the cyclopropyl ring. Computational analysis of the bicyclic PMP derivatives 1,2,3-trimethylenecyclohexane-4,6-diyl and 2,6-dimethylene- cyclohexanone-3,5-diyl indicates that they have 3B2 ground states which are less than 2 kcal/mol compared to their corresponding diradical 1A1 states.

Spectroscopic studies of the picosecond dynamics of the photoreaction of an artificial bacteriorhodopsin (BR) pigment with a retinal show that C-13=C-14 isomerization is the key step in the BR photocycle. Motion in the C-12=C-13 and C-13=C-14 regions are essential for the formation of K-like intermediate in the native BR-570 photocycle, but are not required to form an intermediate with spectral and kinetic properties similar to that of J-625 in the BR photocycle.

Examination of simultaneous nonenzymatic hydrolysis and isomerization of 3',5''-uridyluridine and related dialkyl phosphates, the RNA models, in aqueous morpholine buffers helps suggest an alternative mechanism. Kinetic equations generated by this alternative mechanism reproduce the experimental data. The mechanism also accounts for the dependence of kinetics on pH.

Al initio studies on the stability of two tautomeric phosphorus hydrides, H2PPH2 and HPPH3, reveal the higher thermodynamic stability of H2PPH2 than HPPH3, while semiempirical calculations suggests a reverse order of thermodynamic stability. High temperature favor decomposition of H2PP2 rather than its transformation to HPPH3. High barrier for unimolecular tautomerization is responsible for the high stability of an isolated HPPH3 molecule.

Analysis of the structures of two misdirected ligand complexes of Ru and Os reveals that they are isostructural. Kinetic studies of atropisomerization of these complexes reveals that metal-biisoquinoline bond strength significantly influences the rate of atropisomerization. Kinetic and thermodynamic data reveal the redirection of the misdirected 1,1'-biisoquinoline ligand in the syn planar transition state. Kinetic lability of metals, which form thermodynamically stronger M-N bonds, is higher with respect to atropisomerization of the 1,1'-biisoquinoline ligand.

Ab initio calculation at the MP2/6-31G* level helps determine equilibrium geometries and harmonic vibration frequencies of various cyanates, isocyanates, nitrile oxides, and CN- or NC-substituted fulminates and their sulfur and selenium analogues. A comparative study of the stabilities of different isomers and the transition state associated with these isomers suggests isomerization pathways between the stable structures.

GC-Fourier transform infrared and GC-MS analyses of the stereochemistry, structure and thermal isomerization of sex pheromones of male longhorn beetle Anaglyptus subfaciatus show that 3-hydroxy-2-hexanone and 3-hydroxy-3-octanone are the pheromone constituents present as a molar mixture in the ratio 7:1. These compounds thermally isomerize to yield their respective 2-hydroxy-3-alkanones. The two semiochemicals display (R)-stereochemistry.

Experimental studies involving in situ preparation and trapping of a diazo compound enable the preparation of the isomers, (5,6) fulleroid and (6,6) methanofullerene. Kinetic studies reveal that the substrate concentration exerts no influence on the rate of conversion between these isomers. Cyclic voltammetry reveals that fulleroid undergoes reduction at 34 mV more positive potential than methanofullerene.

The addition of tpy to (NBu4)(OS(N)CL4) in dichloromethane results in trans-(OS(tpy)(Cl)2(N))Cl (1). The cis isomer is isolated as its (PF6)-salt from a methanolic solution of 1 in the presence of chloride ions and the solution attains equilibrium via first order kinetics. Isomerization involves an associative attack of methanol, forming a seven co-ordinate intermediate and is not feasible in dichloromethane.

Examination of the photophysical and photochemical characteristics of a series of trans-(aminoalkyl)stilbenes indicates that tertiary(aminoalkyl)stilbenes form fluorescent exciplexes and undergo trans-cis isomerization, while it does not undergo intramolecular reactions. Temperature, solvent and linker influence the photophysical behavior of tertiary (aminoalkyl)stilbenes. Secondary (aminoalkyl)stilbenes undergo intramolecular addition, while they do not form fluorescent exciplexes. These intramolecular reactions are selective and form tetrahydrobenzazepines. Primary (aminoalkyl)stilbenes undergo only trans-cis isomerization, while they undergo intramolecular addition upon irradiation in the presence of the electron-acceptor p-dicyanobenzene.

Gas chromatography-mass spectrometry facilitates the identification of stereoisomers of Delta 3,Delta 5-dienoyl-CoA's formed during the oxidation of Delta 5-unsaturated fatty acids. An intermediate in the oxidation, trans-2,Delta 5-dienoyl CoA, undergoes isomerization to Delta 3, Delta 5-dienoyl-CoA's, catalyzed by acyl-CoA oxidase. Acyl-CoA oxidase fails to isomerize trans-2,trans-5-dienoyl-CoA.

Analysis of a series of Mo(CO)(6-n)(dmpi)n compounds (n = 1-6 and dmpi = 2,6-dimethylphenyl isocyanide) by cyclic voltammetric and IR spectroelectrochemical studies enables the identification of cations formed during oxidation and the determination of E1 2 values for the first oxidation of the Mo isocyanides. Molecular orbital calculations and 95Mo NMR experiments agree with the E1 2 values. Experimental data indicate the observation of fac-mer and cis-trans isomerizations in two members of the series, n = 3 and 4. Digital simulations help calculate the rate constants for the isomerization reactions.

Addition of 2 equiv of ClAuPPh3 to deprotonated Mn2(Mu-H)(mu-PCyH)(CO)8 produces an equilibrium mixture of mu3-bridged product and mu4-bridged cluster. Single-crystal X-ray studies help determine the structure of the mu3-bridged compound and 31P NMR helps characterize the mu4-bridged compound. A permanent valence isomerization of heteronuclear metal-metal bonds occurs in the mu4-bridged cluster. The dependence of isomerization on residues R and solvent polarity is analyzed.

Molecular mechanics calculations on the cis-trans imide isomerization of the proline dipeptide reveal the involvement of the proline backbone torsion angle, the pyramidalization of the imide nitrogen and the imide bond torsion angle in the isomerization process. Isomerization are better explained by the dihedral angle than by the torsion angle. Ab initio studies reveal the significant influence of torsion angle on the activation barrier. Interactions at zero torsional angle reduce the activation barrier and this autocatalytic transition state stabilization is vital for catalytic pathway in rotamases.

Neutron diffraction studies of the positional oscillation of the deuterium labels of bacteriorhodopsin (BR) in the beta-ionone ring (D11) and adjacent to the Schiff base (D5), between the BR568 ground state and the M412 photocycle intermediate, reveals that the transition from BR568 to M412 does not affect the D11 ring position in the projected structure. The D5 label moves closer to the D11 ring by 1.4 plus or minus 0.9 angstroms. The reduction in interlabel distance indicates that the C-5 to C-13 portion of the polyene chain gets out of the membrane plane by 11 degrees plus or minus 6 degrees toward the cytoplasm during the BR568-M412 transition due to the all-trans/13-cis isomerization.

Photocycloaddition reactions enable the conversion of hexafluorobenzene into 1,2- and 1, 8-dichloroperfluorocyclooctatetraenes, the stable bond-shift isomers. 19F NMR experiments enable the determination of the kinetic and thermodynamic parameters of the interconversion between the isomers. High temperature studies reveal the absence of skeletal rearrangement in the isomerization process. UV irradiation and triplet sensitization increase the rate of interconversion, while exposure of the reaction mixture to UV light for a longer time leads to photocyclization.

Picosecond optical calorimetric and fluorescent studies of the photoisomerization of tetraphenylethylene help understand the structure-kinetic and structure-energy relations in the excited twisted state. These studies indicate the presence of three excited states, which provide a pathway for the potential energy surface along the photoisomerization coordinate.

Picosecond fluorescence and two-step LIF spectroscopies of methanol solutions of 3-hydroxyxanthone and 7-hydroxyflavone indicate a large Stokes-shifted fluorescence due to the tautomer and the anion. The excited states of 1:2 methanol H-bonded compounds generate the tautomer, while the excitation of the 1:1 methanol complex gives the anions. These studies are not sufficient to enable a structural characterization of the anion and the tautomer.

Protonation of Cp*Rh(C2H4)2, where Cp* is C5Me5, yields a selective Rh(III) catalytic system capable of inducing linear dimerization of methylacrylate. Kinetic studies and analyses of C-C coupling and catalyst resting state at low temperatures reveal the mechanism of dimerization. Use of iridium analogs in the reaction supports the mechanism. Substitution of methylated indenyl ligands for the C5Me5 ligand causes secondary generation of catalysts with higher catalytic activities and longer lifetimes.

A study of the relationship between proline cis-trans isomerization and multiple conformations in salmon calcitonin (sCT) reveals that resonance heterogeneity for nearby amino acids is stimulated by the isomerization of Pro23. The structure of the sCT hormone influences the cis-trans ratio. The sCT exhibits a 35% cis population in water but decreased to 16% in the folded SDS-bound hormones. The decrease indicates a Gibbs-free energy stabilization of 3.1 kJ per mole in the conformation of the hormones.

NMR studies of cis-bis(5'GMP)-platinum(II)-diamine complexes containing asymmetric diamine ligands reveals that both NH groups direct to one side of the coordination plane. Nuclear Overhauser effect studies reveal that the coordination between 5'GMP and two non-equivalent Pt coordination sites occurs through N7. Spectroscopic studies help examine atropisomerization in these complexes due to restricted rotation of Pt-N7 bonds. Factors such as hydrogen bonding influence the conformation and ratio of atropisomers.

ZP(MeNCH2CH2)3N, where Z is a lone pair, catalyzes the trimerization of isocyanates to form perhydro-1,3,5-triazine-2,4,6-triones at low concentrations of 0.0033 mol%. Analysis of the catalyst's lifetime reveals that it can be reused at least six times without degradation. Two other compounds Ch double bond P(MeNCH2CH2)3N, (Ch is O, S), are better catalyst for the conversion of isocyanates to carbodiimides than their acyclic analogues. Structural studies show that the P-N(ax) transannulation influences catalytic properties.

Examination of mixed-lithium diisopropylamide and potassium tert-butoxide-promoted isomerization of alkoxy-substituted oxiranes to hydroxy-substituted ene ethers shows the influence of the structure of oxirane substrate on the stereoselectivity of the reaction. Disubstituted oxiranes produce E-ene ether preferentially, while trisubstituted oxirane, depending on the position of the third substituent, either produces only E-ene or a mixture of stereoisomers.

A substituted cyclohexanone helps synthesize dispiro(4.0.4. 4)tetradeca-11,13-dienes having one or two heteroatoms. Steric and electronic factors influence acid-catalyzed isomerization of these dienes and control the choice between aromatization and (4.4.4)propelladiene. Formation of transient oxonium ion favors both pathways equally, but oxygen and sulfur atoms control the choice of competitive reaction.

An m-MeO group labels the rings of trimesitylvinyl isopropyl ether to measure four barriers to helicity reversal, which is due to a correlated rotation of the three aryl rings. Three-ring flip exhibits a lower barrier while two-ring flip process, associated with C double bond C plane, exhibits a higher barrier. MM calculations of the ground state structure is in good agreement with the X-ray structure while calculated transition states are lower due to ring distortions from planarity.

Ab initio calculations of the isomerization of substituted benzenes and (6)paracyclophanes to Dewar benzene isomers reveal the destabilized nature of the benzene form when compared to the Dewar form, on substitution with electron donors and acceptors. The trend of the reaction enthalpies of (6)paracyclophanes is explained using an additional steric effect. The isomerization enthalpy of HMB is lower than that of the benzene. The results agree well with experimental isomerizations of HMB and PFHMB.

Solvent fluctuation controls thermal isomerizations in highly viscous mediums associated with high activation energies. A two-step mechanism explains the isomerization kinetics. The key process step is the rearrangement of solvent molecules to form cavities, followed by dual steric transformations. Viscosity influences the rate-determining step.

A cis-trans equilibrium mixture resulted when a bis(pentafluorophenyl)bis(tetrahydrothiophene)palladium(II) complex isomerized in chloroform. Tetrahydrothiophene dissociative loss characterized the isomerization mechanism, in which specific three-coordinate intermediates interconverted. These complexes were used for several palladium-catalyzed organic reactions.

Ab initio methods are employed to analyze the strength of binding in the H2O.SO3 intermediate complex, its isomerization barrier and its conversion to H2SO4. There is a significant difference between calculated and literature values. The medium influences the intermolecular distance in the bimolecular complex and polarization reorganizes electron distribution. Water molecules facilitate the formation H2SO4.

The diastereomeric isomerization of a ruthenium complex having a 1,1'-binaphthyl skeleton involves a atropisomerization of the eta(super 2)-1,1'-biisoquinoline ligands. Kinetics and mechanistic study reveal the formation of a syn transition state. Transition state structure is stabilized by the Ru-N band strength, which remains intact during the isomerization.

Cycloisomerization of 1,6- and 1,7-enynes to dialkylidenecyclopentanes and -cyclohexanes is achieved by the employing palladium(O), acetic acid and a ligand. The reaction mechanism is compared with the reaction catalyzed by palladium acetate. Palladium acetate reaction involves a Pd(+2) to Pd(+4) cycle and a hydridopalladium acetate mechanism is involved in the present reaction. Steric effects and an electronic effect are vital in favoring 1,3- over 1,4-diene formation.

1, 2-dialkylidenecycloalkanes are efficiently prepared by the palladium-catalyzed cycloisomerization of enynes to 1,3-dienes. Incorporation of dienophile into the substrate leads to polycyclization by simple cycloisomerization. Steric factors influence the regioselectivity of the reaction.

Cluster skeleton reorganization of B6H10 is analyzed to obtain all possible intramolecular mechanisms. The degenerate cage rearrangement mechanisms reveal the participation of a tetragonal pyramid intermediate, B5H8(BH2), through a diamond-sequence-diamond reorganization. The isomerization process in the iridaborane, ((IrB5H8)(CO)(PH3)2), proceeds through a C2(6,0;4,0,0)-like mechanism and the highest barrier for the isomerization is the DSD rearrangement.

15N nuclear magnetic resonance spectroscopy is used to follow the N-1 to N-2 rearrangements of (5-methyltetrazolato)pentaamminecobalt(III) complexes. The linkage isomerization is found to be intramolecular in Me2SO and water as solvents. These rearrangements are acid-catalyzed and the ligand never leaves the metal ion.

The synthesis and reactions of several N-methyltropan-3-ylindoles, which were designed as congeners of ibogaine, were described through a mechanism that involved an exocyclic enamine tautomer of the indole ring as the intermediate. The presence of increased strain in the endobicyclic 2-substituent caused a decrease in the relative energy of the exocyclic enamine tautomer.

A study of geometrical isomerization and restricted rotation in iminoxyl radicals from benzaldoximes revealed that the rotational barrier had a value of 6.18 kilocalories per mole. Tert-butoxy radicals, which were photolytically produced, facilitated the oxidation of E geometrical isomers of benzaldoxime P-chlorobenzaldoxime and P-methylbenzaldoxime to the corresponding iminoxyl radicals.

The active site of isopentenyl diphosphate dimethylallyl diphosphate isomerase (EC 5.3.3.2) contains Gly207 and Cys139, essential for catalysis. Addition of 3-(fluoomethyl)-3-butenyl diphosphate to C139S mutant inactivates the enzyme covalent regulation of E207. The E207V and E207 Q mutants are inactive, while Cys139 and Glu207 activate site-directed mutagenesis.

Isomerization between open and closed states of the IR channel is allosterically modulated by occupancy of binding sites for K+ and related activator ions. The rates of opening and closing exist as functions of voltage and ion concentrations. Occupancy of the pore by Rb+ can modify the rates of isomerization and the affinity of the allosteric sites for activator ions. Binding sites that regulate gating are different from those governing permeation as Rb+ has lower permeability than K+.

Photoisomerization modulates the cation-binding ability of crowned spironaphthoxazine, in the presence of Li+ salt, due to an additional binding-site effect that occurs in its open colored form. Systems that control photochemical cation-binding with crowned spironaphthoxazine may be applied to ionic-conductivity switching, ion transfer and photoinduced membrane transport of ionic species.

6-31G* level-based CASSCF studies of the interaction between the ground and excited-state surfaces in s-trans-and s-cis-acrolein yield two varying, photochemically active paths originating from a planar excited-state minimum. The first pathway includes a radiationless decay-derived intermediate, whose decay induces acrolein double-bond isomerization. The second path exclusively involves the singlet mainfold. The results are consistent with the photochemistry of alpha, beta-enones.

The total synthesis of the chorismic acid isomer, trans-3-((1-carboxyvinyl)oxy)-6-hydroxycyclohexa-1,4-diene-1-carboxylic acid proceeds via a two-step pathway involving (3,3)-sigmatropic rearrangement and aromatization. The 1,4-diene's Claisen rearrangement is so much faster than that of chorismate that standard kinetic studies are impossible. There is an alternate pathway for the Claisen rearrangement of the 1,4-diene.

Low-resolution studies of Streptomyces olivochromogenes D-xylose isomerase enzyme-substrate complex's lack of solvent-isotope exchange enzyme catalyzed reaction suggests a non-proton transfer mechanism. A hydride transfer mechanism possibly mediates the enzyme action and may occur after ring opening. Enzyme bound magnesium and manganese do not interact with any single specific glucose site and indicate both productive and nonproductive binding modes for substrate glucose.

CAS-SCF and CAS-SCF/MP2 studies using the 4-31G and DZ+d basis sets yield two reaction pathways for the excited-state cis-trans isomerization of cis-hexatriene. Reaction coordinate calculations reveal that the pathways relate to c by t and Z by E conversions of the initial isomer. The results prove that the reaction is nonadiabatic. The reactions pass over small barriers and terminate in two separate Born-Oppenheimer violation domains.

UV, IR and NMR spectroscopic studies on cobalt(III)pentaammine complexes of 2-pyridone as O- and N-bonded linkage isomers reveal that the O-bonded 2-pyridone complex is most stable. The N to O rearrangement for protonated complexes is complete in water. The isomerization is slower and reversible in Me2SO4.

Absorption spectroscopic and flash photolytic studies on the retinal bacteriorhodopsin (BR) reveal that it can function without a covalent linkage between the retinal and the protein. The chromophore's absorption maximum red shift and the thermal 13-cis to all-trans isomerization reaction proceed independently. BR interactions are predominantly electrostatic in nature.

Spectroscopic, enzymative and flash photolytic studies on rhodopsin-catalyzed visual transduction process reveal that the process is triggered by a total 11-cis to all-trans isomerization of rhodopsin, involving the entire rigid polyene motif. The experiments use methylated Rh that contain the 11-cis-locked eight-membered ring retinal 8 (MeRh8). UV-visual and CD spectra reveal that MeRh8 and native Rh have similar chromophoric domains.