Qi-yuan Zhang

Studies of the solvent effects on the internal reorganization energy for electron transfer of uracil and its anion with ONIOM

Abstract In this paper, the aqueous adiabatic electron affinity (AEA) of Uracil (U) and internal reorganization energy λ i of the self-exchange electron transfer (ET) reaction between Uracil and Uracil anion radical (U − ) in aqueous solution were studied. The effect of the solvation was studied with the recently developed hybrid quantum molecular chemical method, ONIOM. In all calculations, the geometrical optimization for U and U − was performed at B3LYP/6-31++G(d) level. As for the solvent surroundings, the seven water molecules as the first hydration shell were adopted and treated with B3LYP, PM3 and AMBER methods, namely, ONIOM (B3LYP:B3LYP), ONIOM (B3LYP:PM3) and ONIOM (B3LYP:Amber) methods, respectively. The values of AEA for Uracil, predicted by the above three methods, are small positive ones. The geometrical differences between neutral and anion radical molecules of U originate mainly from those of dihedral angles. According to the corresponding dipole moment values, the excess electron in U − should be trapped dominantly by dipole-bound way. The calculated λ i values by ONIOM (B3LYP:B3LYP) and ONIOM (B3LYP:PM3) are close to each other within 0.89%. The λ i value from ONIOM (B3LYP:Amber) is in agreement with the one from SCRF-CPCM very well. Finally, the calculation results of the detailed geometries and molecular interaction mode effect of U and U − and related water molecules in the hydration shell were discussed.

Theoretical studies on the mechanism of primary electron transfer in the photosynthetic reaction center of Rhodobacter sphaeroides.

The mechanism of the primary electron transfer (ET) process in the photosynthetic reaction center (PRC) of Rhodobacter sphaeroides has been studied with quantum chemistry method of ab initio density functional theory (DFT) (B3LYP/6-31G) based on the optimized X-ray crystallographic structure. The calculation was carried out on different structural levels. The electronic structure of pigment molecules was first studied, and then the influence of the neighboring protein was taken into account at three approximation levels: (a) the surrounding proteins were treated as a homogeneous medium with a uniform dielectric constant (SCRF); (b) both the influence of axial coordination of His to the special pair P and ABChl as, and the hydrogen bonds between related residues and P and also BPhas were included; and (c) the influence of the electronic structure of the protein subunit chains as a whole was studied. The results suggest that: (1) according to the composition of the HOMO and LUMO of P, there might be a charge-separated state of (BChlL+BChlM−) for the excited state of P; (2) to treat the protein surroundings as a homogeneous medium is not sufficient. Different interactions between pigment molecules and related residues play different roles in the ET process; (3) the axial coordination of His to P raises the ELUMO of P greatly, and it is very important for the ET process to occur in the PRC of wild-type bacterium; the axial coordination of His to ABChl as also raises their ELUMO significantly; (4) the hydrogen-bonds between amino acid residues and P and also BPh as depress the ELUMO of the pigment molecules to some extent, which makes the ELUMO of P lower than those of ABChlas, and the ELUMO of BPh aL lower than that of BPh aM. Consequently, the ET process from P to BPh aL does not, according to our calculation model, occur via ABChl aL. The possibility of the ET pathway from P to BPh aL via ABChl aL was discussed; (5) the frontier orbitals of protein subunit chains L and M are localized at the random coil area and the α–helix areas, respectively. Results mentioned above support the fact that the ET process proceeds in favourable circumstances along the branch L.

The isonitrile-nitrile isomerization: kinetic parameters, reaction mechanism and relative photoionization cross-section of the HOMO. A HeI photoelectron spectroscopy study

Abstract The isomerisation reactions from CH 3 CH 2 CH 2 NC to CH 3 CH 2 CH 2 CN, (CH 3 ) 2 CHNC to (CH 3 ) 2 CHCN and (CH 3 ) 3 CNC to (CH 3 ) 3 CCN are found to be of first order by using HeI photoelectron spectroscopy (PES). The activation energies obtained by PES for the isomerisation of RNC, where R is −CH 3 , −CH 2 CH 3 , −CH 2 CH 2 CH 3 , −CH(CH 3 ) 2 , and −C(CH 3 ) 3 are similar. This can be explained by the breaking of the RN bond and the making of the RC bond in the isomerisation reaction from RNC to RCN being essentially synchronous. A transition state is proposed. The photoionization cross-sections of the HOMO for the RNC are deduced from the intercept values in the kinetic equations obtained using PES, and related to the weight of the carbon atom in the isocyano group, because the HOMOs of the RNC mainly embody the 2s lone-pair electron of the carbon atom in the isocyano group.

Theoretical study on the mechanism of the reaction between CN and O2

Abstract The radical–radical reaction between CN ( 2 Σ) and O 2 ( 3 Σ g ) has been theoretically investigated at the UCCSD(T)/6-311+G(d)//UB3LYP/6-31+G(d) level. This reaction proceeds most likely through the doublet CNO 2 potential energy surface (PES) initiated by the carbon-to-oxygen attack leading to the linear NCOO ( 2 A ″) radical, followed by the direct oxygen–oxygen single-bond cleavage leading to (A) OCN ( 2 Σ)+ O ( 3 P ) , or by the sequential three-centered isomerizations and final dissociations leading to (B) CO ( 1 Σ)+ NO ( 2 Π) and (C) CO 2 ( 1 Σ g )+ N ( 2 D ) . This study may be helpful for understanding the combustion chemistry of nitrogen-containing compounds.

Theoretical study on the mechanism of the reaction: HCCCH2++C2H2→c-C3H3++C2H2

Abstract The gas phase ion–molecule reaction of propargylium ( HCCCH 2 + ) with acetylene (C2H2) to produce cyclopropenylium (c -C 3 H 3 + ) with C2H2 has been investigated theoretically at the B3LYP/6–31G(d) and single-point QCISD/6–311G(d,p) levels. The detailed mechanism for the observed isotope exchange between HCCCH 2 + and C2D2 has also discussed. Three intermediates 1 CH2CCH2CCH+, 2 H 2 C 2 · CHCCH 2 + and 3 c -C 4 H 3 –CH 2 + are shown to play important roles in the product formation and isotope exchange processes, rather than the low-lying isomers 4 c -C 3 H 2 –CH 2 + , 7 c - ( CH ) 5 + and 8 pyramidal C 5 H 5 + . Our calculated results agree well with the available experimental data and may be helpful for understanding the mechanism for combustion processes.

Density functional investigation on electron‐transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism

The mechanism of cycloreversion of cyclobutane radical anion (c‐C4H  8− ) has been investigated at the UB3LYP/6‐31++G(d,p) level, and compared with those of neutral c‐C4H8 and c‐C4H  8+ radical cation. Although both c‐C4H  8− and C2H4 are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the “rotating” cycloreversion of c‐C4H  8− (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c‐C4H8, and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c‐C4H8 by about 8.4 kcal/mol, mainly due to stronger electron‐deficiency of intermediate biradical species than close‐shell cyclobutanes. For the cycloreversion for c‐C4H  8− , side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron‐attachment catalysis of the cycloreversion of some electron‐deficient substituted cyclobutanes.

The reaction of formaldehyde with chlorine atom

Abstract The elementary reaction of formaldehyde (H2CO) with chlorine atom has been experimentally investigated by the time-resolved infrared emission spectroscopy. The nascent products HCO and HCl (v⩽3) are observed. The major product channel has been identified as Cl+H2CO→HCl+HCO. Theoretical calculations have revealed that the mechanism is a nearly barrierless peripheral hydrogen abstraction reaction.

Theoretical investigation on the reaction of ionized water with ethylene

The mechanism for the reaction of H2O+ with C2H4 has been investigated theoretically at the UCCSD(T)/6-31++G(d,p)//UB3LYP/6-31++G(d,p) level. Two major products (A) H2O+C2H4+ and (B) HO+C2H5+ are shown to be formed through the parallel reactions of charge-transfer and proton-transfer via the respective intermediates of (a) H2O·C2H4+ and (b) HO·HC2H4+. The dissociation of intermediate (c) HOC2H5+ resulting from the 1,3-H-shift of (a), may lead to the minor product (C) HOCH2++CH3. The calculated results agree well with the available experimental data and may be helpful for understanding the chemical behavior of analogous radical cations containing H–O bond.

Theoretical study on the mechanism of the gas-phase reaction of diborane(3) anion with carbon disulfide.

The complex potential energy surface of the gas‐phase reaction of HB(H)BH− with CS2 to give three low‐lying products [B2H3S]−+CS, [BH2CS]−+HBS, and [BH3CS]+BS−, involving nine [B2H3CS2]− isomers and 12 transition states, has been investigated at the CCSD(T)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) level. Our calculations are in harmony with the recent experimental and theoretical results, and reveal some new bonding and kinetic features of this reaction system. Our theoretical results may help the further identification of the products [BH2CS]−+HBS and [BH3CS]+BS− and may provide useful information on the chemical behaviors of other electron‐deficient boron hydride anions.

Energy transfer kinetics of phycoerythrocyanin trimer from cyanobacteriumAnabaena variabilis (II).

The excitation energy transfer processes in trimeric PEC have been studied by using steady-state and time-resolved fluorescence spectra techniques in detail. The results indicate that the energy transfer processes should take place between α84-PVB and β84-or β155-PCB chromophores with the time constants 34.7 ps and 175–200 ps individually; in contrast with monomeric PEC, from time-resolved fluorescence anisotropic spectrum technique, the decay constant of 45 ps which was assigned to the energy transfer time among three β84-PCB chromophores was observed and the energy levels of β84-and/or β155-PCB chromophores were confirmed to turn over in trimeric PEC.