Direct observation of deuterium migration in crystalline-state reaction by single crystal neutron diffraction IV. "Hula-twist" rotation of a long alkyl radical produced by photoirradiation

When the crystal of [(R)-1,2-bis(ethoxycarbonyl)ethyl](pyridine)bis(dimethylglyoximato)cobalt(III) was exposed to a xenon lamp, the chiral 1,2-bis(ethoxycarbonyl)ethyl group was partly inverted to the opposite configuration and finally the racemic group was produced with retention of the single crystal form. To make clear the mechanism, the hydrogen atom bonded to the chiral carbon of the chiral group was exchanged with the deuterium atom and the crystal was exposed to the xenon lamp for 3 days. The crystal after irradiation was analyzed by neutron diffraction. About 33% of the (R)-isomers were inverted to the (S) isomers in a crystal. The deuterium atom in the (S)-isomer was bonded to the same chiral carbon atom. This result clearly indicates that the inversion proceeds in the three steps; (i) the Co-C bond was homolytically cleaved by photoirradiation and the 1,2-bis(ethoxycarbonyl)ethyl radical and Co(II) were produced, (ii) the radical rotated by 180 degrees directing the C-D bond to the cobalt atom and the opposite plane of the radical faced to the cobalt atom, and (iii) the radical made a bond with Co(II). Because the peripheral atoms of the long radical occupy approximately the same positions in the process of the radical rotation, the crystal was not decomposed. The above rotation is a good example of hula-twist rotation in the process of photoisomerization of polyenes such as rhodopsin.     

Isomerism and adduct formation in the Hector''s base series: A MNDO study of model compounds

MNDO calculations on a series of a model compounds show that the observed structures for Hector's base, Dost's base and Dost's keto compound are the thermodynamically most stable tautomers and that the bond-switched structure observed for the 1:1 adduct of Hector's base with carbon disulphide and the non-bond-switched structure observed for the corresponding adducts with isocyanates and isothiocyanates are both the thermodynamically most favoured isomers, so that the occurrence or otherwise of a bond switch in these compounds is determined by thermodynamic rather than by mechanistic factors. Proposed mechanisms for the formation of the carbon disulphide adduct of Hector's base, and for its desulphurisation are supported by MNDO calculations.     

Iron catalyzed polyethylene chain growth on zinc: a study of the factors delineating chain transfer versus catalyzed chain growth in zinc and related metal alkyl systems

The bis(imino)pyridine iron complex, [[2,6-(MeC=N-2,6-iPr2C6H3)2C5H)N]FeCl2] (1), in combination with MAO and ZnEt2 (> 500 equiv.), is shown to catalyze polyethylene chain growth on zinc. The catalyzed chain growth process is characterized by an exceptionally fast and reversible exchange of the growing polymer chains between the iron and zinc centers. Upon hydrolysis of the resultant ZnR2 product, a Poisson distribution of linear alkanes is obtained; linear alpha-olefins with a Poisson distribution can be generated via a nickel-catalyzed displacement reaction. Other dialkylzinc reagents such as ZnMe2 and ZniPr2 also show catalyzed chain growth; in the case of ZnMe2 a slight broadening of the product distribution is observed. The products obtained from Zn(CH2Ph)2 show evidence for chain transfer but not catalyzed chain growth, whereas ZnPh2 shows no evidence for chain transfer. The Group 13 metal alkyl reagents AlR3 (R = Me, Et, octyl, IBu) and GaR3 (R = Et, nBu) act as highly efficient chain transfer agents, whereas GaMe3 exhibits behavior close to catalyzed chain growth. LinBu, MgnBu2 and BEt3 result in very low activity catalyst systems. SnMe4 and PbEt4 give active catalysts, but with very little chain transfer to Sn or Pb. The remarkably efficient iron catalyzed chain growth reaction for ZnEt2 compared to other metal alkyls can be rationalized on the basis of: (1) relatively low steric hindrance around the zinc center, (2) their monomeric nature in solution, (3) the relatively weak Zn-C bond, and (4) a reasonably close match in Zn-C and Fe-C bond strengths.     

Multidimensional reaction coordinate for the excited-state H-atom transfer in perylene quinones: importance of the 7-membered ring in hypocrellins A and B

The excited-state intramolecular H-atom transfer reactions of hypocrellins B and A are compared by using time-resolved absorption and fluorescence upconversion techniques. The hypocrellin B photophysics are well described by a simple model involving one ground-state species and excited-state forward and reverse H-atom transfer with a nonfluorescent excited state. We suggest that excited-state conformational changes are coupled to the H-atom transfer in hypocrellin B just as gauche/anti changes are coupled to the H-atom transfer in hypocrellin A.     

Indium as a radical initiator in aqueous media: intermolecular alkyl radical addition to CN and CC bond

The carbon-carbon bond-forming method in aqueous media was investigated by using indium as a single-electron transfer radical initiator. The indium-mediated intermolecular alkyl radical addition to imine derivatives and electron-deficient CC bond proceeded effectively.     

Bis(imino)pyridine cobalt alkyl complexes and their reactivity towards ethylene: a model system for beta-hydrogen chain transfer

Bis(imino)pyridine cobalt(I) n-alkyl complexes react with ethylene by beta-hydrogen transfer, allowing direct study of a termination step commonly encountered in polymerisation and oligomerisation catalysis.     

Coarse-grained polyethylene: Including cross terms in bonded interactions and introducing anisotropy into the model for the orthorhombic crystal

Our previous paper (E.A. Zubova, I.A. Strelnikov, N.K. Balabaev, A.V. Savin, M.A. Mazo, and L.I. Manevich, Polym. Sci., Ser. A 59 (1) (2017)) addressed the simplest coarse-grained model of polyethylene and alkanes. The CH₂ group in this united-atom model is replaced with a bead. In the framework of the model, nonbonded interactions are described by the Lennard-Jones potential (6–12), whereas the potential for bonded interactions accounts for the bonds between beads and for coarse grained angles and dihedral angles but not for the cross terms between them. We found the area of geometrical parameters of the model where all the three known crystalline phases of polyethylene are stable at low temperatures. We parametrized the force field of the model using the dynamic properties of the system, namely, the inelastic neutron scattering spectrum of the orthorhombic phase of polyethylene. However, the simplest model underestimates the value of the elastic modulus along the chains of the crystal by a factor of two. The derived setting angle of the molecules also differs appreciably from the experimental data. Moreover, the acoustic dispersion curves for the modes with the wave vector directed along the chain axis deviate from the experimental data at low frequencies. In the present study, we included the cross terms into the bonded interactions. This made it possible to reproduce the experimental elastic modulus along the chains of the crystal and to decrease the frequency range for the optical skeletal dispersion curve to proper values. As for the beads, we separated force centers for the bonded and nonbonded interactions, which enabled us to reproduce the optical skeletal curve and to bring the anisotropy of interchain interactions in line with the experiment. However, the model fails to reproduce the balance of interactions between the neighboring chains in the crystal. For this, a different form of the potential energy of van der Waals interactions seems to be needed.     

Reactions of mono- and bimolecular hydrogen transfer in alkyl radicals: analysis using the parabolic model and density functional calculations

Experimental data on monomolecular hydrogen transfer in the reactions of the type RC^·H(CH₂)_nCH₂R¹ RCH₂(CH₂)_nC^·HR¹ (n = 2—4, R and R¹ are alkyl substituents) were analyzed using the parabolic model (PM). The parameters characterizing this class of reactions were calculated. Isomerization of alkyl radicals via cyclic transition states (TS) is characterized by the following energy barriers to thermoneutral reaction E _e0: 53.5, 65.4, and 63.2 kJ mol^–1 for the six-, five-, and seven-membered TS, respectively. The E _e0 energy and the strain energy change in parallel in the series of cycloparaffins C_nH_2n. Density functional calculations of intramolecular hydrogen transfer in the n-butyl and n-pentyl radicals and of the bimolecular hydrogen abstraction from the ethane molecule by the ethyl radical were performed. The activation energies of the intra- and intermolecular hydrogen transfer were compared. The parameters of the PM were compared with the interatomic distances in the reaction center of the TS calculated by the density functional method.     

Charge transfer in polypeptides: effect of secondary structures on charge-transfer integral and site energies

We have theoretically studied the charge transfer in glycine polypeptide using quantum mechanical models based on a tight-binding Hamiltonian approach. The charge-transfer integrals and site energies involved in the transport of positive charge through the peptide bond in glycine polypeptide have been calculated. The charge-transfer integrals and site energies have been calculated directly from the matrix elements of the Kohn-Sham Hamiltonian defined in terms of the molecular orbitals of the individual fragments of the glycine polypeptide. In addition to this, we have calculated the rate of charge transfer between a neighboring amino acid subgroup through the Marcus rate equation. These calculations have been performed for the different secondary structures of the glycine model peptide such as linear, alpha-helix, 3(10)-helix, and antiparallel beta-sheet by varying the dihedral angles omega, varphi, and psi along the Calpha-carbon of amino acid subgroup. Present theoretical results confirm that the charge transfer through the peptide bond is strongly affected by the conformations of the oligopeptide.     

A model calculation on the transport of excitation energy in a molecular crystal

We report a model calculation of the transport of a local (site) excitation in a doped molecular crystal containing one impurity. We do not consider the impurity as a direct trap for electronic excitations (zero trap depth) but assume that exciton-phonon interaction is exclusively given by the coupling of excitons with the vibrational displacement of the impurity. The dynamical problem is solved by using a time-dependent effective potential consisting of equilibrium average exciton-phonon interaction and fluctuations around this average. Two correlation functions are computed using the slow phonon limit and assuming that the temperature of the system is 300 K. Transmission of the excitation energy over a distance of eight spacings takes place, electronically, within a few picoseconds. With the exciton-phonon interaction switched on, calculated correlation functions diminish very rapidly with increasing time, indicating that an irreversible transfer of excitonic energy to the thermal bath takes place. Thus transmission of the excitation energy over such a distance (and without a high rate of trapping) is not an efficient process.     

Electron transfer between a tyrosyl radical and a cysteine residue in hemoproteins: spin trapping analysis

We investigated electron transfer between a tyrosyl radical and cysteine residue in two systems, oxyhemoglobin (oxyHb)/peroxynitrite/5,5-dimethyl-1-pyrroline N-oxide (DMPO) and myoglobin (Mb)/hydrogen peroxide/DMPO, using a combination of techniques including ESR, immuno-spin trapping (IST), and ESI/MS. These techniques show that the nitrone spin trap DMPO covalently binds to one or more amino acid radicals in the protein. Treating oxyHb with peroxynitrite and Mb with H2O2 in the presence of a low DMPO concentration yielded secondary Cys-DMPO radical adduct exclusively, whereas in the presence of high DMPO, more of the primary Tyr-DMPO radical adduct was detected. In both systems studied, we found that, at high DMPO concentrations, mainly tyrosyl radicals (Hb-Tyr42/Tyr24 and Mb-Tyr103) are trapped and the secondary electron-transfer reaction does not compete, whereas in the presence of low concentrations of DMPO, the secondary reaction predominates over tyrosyl trapping, and a thiyl radical is formed and then trapped (Hb-Cys93 or Mb-Cys110). With increasing concentrations of DMPO in the reaction medium, primary radicals have an increasing probability of being trapped. MS/MS was used to identify the specific Tyr and Cys residues forming radicals in the myoglobin system. All data obtained from this combination of approaches support the conclusion that the initial site of radical formation is a Tyr, which then abstracts an electron from a cysteine residue to produce a cysteinyl radical. This complex phenomenon of electron transfer from one radical to another has been investigated in proteins by IST, ESR, and MS.     

A single transition state serves two mechanisms: an ab initio classical trajectory study of the electron transfer and substitution mechanisms in reactions of ketyl radical anions with alkyl halides

Molecular dynamics has been used to investigate the reaction of a series of ketyl anion radicals and alkyl halides, CH2O(*)(-) + CH3X (X = F, Cl, Br) and NCCHO(*)(-) + CH3Cl. In addition to a floppy outer-sphere transition state which leads directly to ET products, there is a strongly bound transition state that yields both electron transfer (ET) and C-alkylated (SUB(C)) products. This common transition state has significant C-- C bonding and gives ET and SUB(C) products via a bifurcation on a single potential energy surface. Branching ratios have been estimated from ab initio classical trajectory calculations. The SUB(C) products are favored for transition states with short C--C bonds and ET for long C--C bonds. ET reactivity can be observed even at short distances of r(C)(-)(C) = ca. 2.4 A as in the transition state for the reaction NCCHO(*)(-) + CH3Cl. Therefore, the ET/SUB(C) reactivity is entangled over a significant range of the C--C distance. The mechanistic significance of the molecular dynamics study is discussed.     

A note on the accuracy of correlation energy estimation by local approximation: first ionization energies and electron affinities of light atoms

A local spin density functional estimate of the pure correlation energy is added to Hartree-Fock values for the ionization energy and electron affinity of the first eighteen atoms. The local correlation estimate is found to yield a useful improvement in accuracy which augurs well for the application of the same method to molecules.     

A DFT study of H-isomerisation in alkoxy-, alkylperoxy- and alkyl radicals: Some implications for radical chain reactions in polymer systems

Intramolecular 1-n H-shift (n = 2, 3… 7) reactions in alkoxy, alkyl and peroxy radicals were studied by density functional theory (DFT) at the B3LYP/6-311+G∗∗ level and compared with respective intermolecular H-transfers. It was found that starting from 1 to 3 H-shift the barrier heights stepwise decrease with increasing n reaching minimum for 1-5 and 1-6 H-shifts. This dependence can be ascribed to the decrease of the strain with increasing transition state (TS) ring size, which is minimal in six- and seven-member rings. The barrier heights of H-shifts in alkyl radicals are systematically larger than those in alkoxy radicals: the respective activation energies (E_a) of 1-5 and 1-6 H-shifts are about 59-67 kJ/mol for alkyl radical and 21-34 kJ/mol for alkoxy radicals. Further increase of the TS ring size in 1-7 H-shifts leads to the increase of the barrier to 44 kJ/mol in the hexyloxy radical and 84 kJ/mol for n-heptyl radical. We have also found that intermolecular H-transfer reactions in all three types of free radicals have smaller barriers than respective intramolecular 1-5 or 1-6 H-shifts by 4-25 kJ/mol. The mentioned difference can be explained in terms of enhanced nonbonding repulsion interaction in the cyclic TS structures compared to respective intermolecular TS. B3LYP/6-311+G∗∗ geometric parameters and imaginary frequencies for 1-n H-shifts TS are consistent with respective calculated barrier heights. Reactivity of some other radicals compared to alkoxy, peroxy and alkyl radicals as well as other factors influencing their reactivity (π-conjugation, steric effect and ring strain in cyclic TS, etc.) are also briefly discussed in relation to free radical reactions in polymer systems.     

Long-distance radical cation migration in duplex DNA: the effect of contiguous A.A and T.T mismatches on efficiency and mechanism

A series of DNA oligomers was prepared. Each oligomer contained an anthraquinone group (AQ, sensitizer) covalently linked at a 5'-end and two GG steps that surrounded a variable region. The variable region was composed of A.T base pairs or A.A or T.T mismatches. Irradiation of the AQ injected a radical cation (hole) into the DNA that migrated through the duplex, being trapped by reaction with H2O of O2 at the GG steps. The effect of substituting A.A or T.T mismatches for Watson-Crick base pairs was examined. For A.A mispairs, charge transfer through the mismatch region was as efficient as through normal DNA. For the T.T mismatches, radical cation transport was strongly distance-dependent. These findings suggest that A.A mismatches form a zipper-like motif, and charge transport proceeds by a hopping mechanism. In contrast, charge transport through the T.T mismatches (where there are no purines) may proceed by quantum mechanical tunneling.     

Ionization-induced proton transfer in model DNA base pairs: a theoretical study of the radical ions of the 7-azaindole dimer.

Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal-->SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT-->tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7Al)2*- and (7Al)2*+ exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7Al)2*-, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7Al)2*- forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed.     

A model for energy transfer in inelastic molecular collisions applicable at steady state or non-steady state and for an arbitrary distribution of collision energies

A new model for energy exchange between translational and internal degrees of freedom in atom-molecule collisions has been developed. It is suitable for both steady state conditions (e.g., a large number of collisions with thermal kinetic energies) and non-steady state conditions with an arbitrary distribution of collision energies (e.g., single high-energy collisions). In particular, it does not require that the collision energies be characterized by a quasi-thermal distribution, but nevertheless it is capable of producing a Boltzmann distribution of internal energies with the correct internal temperature under quasi-thermal conditions. The energy exchange is described by a transfer probability density that depends on the initial relative kinetic energy, the internal energy of the molecule, and the amount of energy transferred. The probability density for collisions that lead to excitation is assumed to decrease exponentially with the amount of transferred energy. The probability density for de-excitation is obtained from microscopic reversibility. The model has been implemented in the ion trap simulation program ITSIM and coupled with an Rice-Rampsberger-Kassel-Marcus (RRKM) algorithm to describe the unimolecular dissociation of populations of ions. Monte Carlo simulations of collisional energy transfer are presented. The model is validated for non-steady state conditions and for steady state conditions, and the effect of the kinetic energy dependence of the collision cross-section on internal temperature is discussed. Applications of the model to the problem of chemical mass shifts in RF ion trap mass spectrometry are shown.     

On the determination and ramifications of chaos in many-body systems: A model study of polyethylene

Computational methods for elucidating information related to the dynamical behavior of multidimensional systems are presented and applied in the area of macromolecular dynamics. Results indicate that the dimensionality of chaotic dynamics for a model of polyethylene can only be characterized for a very narrow range of extremely low temperature (0–2 K). These results provide evidence that suggests the dynamics of this system are completely chaotic at temperatures as low as 10 K. The preponderance of increasing density of low frequency floppy vibrational modes in large molecular systems provides a facile mechanism for the onset of global chaos. Ramifications of such global chaos to the accurate modeling and simulation of macromolecular dynamics is discussed.