Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Density functional theory study on structural isomers and bonding of model complexes M(CO)5(BH3 · PH3) (M = Cr, Mo, W) and W(CO)5(BH3 · AH3) (A = N, P, As, Sb)

The influence of group 15 various substituents and effect of metal centers on metal-borane interactions and structural isomers of transition metal-borane complexes W(CO)₅(BH₃ · AH₃) and M(CO)₅(BH₃ · PH₃) (A = N, P, As, and Sb; M = Cr, Mo, and W), were investigated by pure density functional theory at BP86 level. The following results were observed: (a) the ground state is monodentate, η¹, with C₁ point group; (b) in all complexes, the η¹ isomer with C_S symmetry on potential energy surface is the transition state for oscillating borane; (c) the η² isomer is the transition state for the hydrogens interchange mechanism; (d) in W(CO)₅(BH₃ · AH₃), the degree of pyramidalization at boron, interaction energy as well as charge transfer between metal and boron moieties, energy barrier for interchanging hydrogens, and diffuseness of A increase along the series A = Sb < As < P < N; (e) in M(CO)₅(BH₃ · PH₃), interaction energy is ordered as M = W > Cr > Mo, while energy barrier for interchanging hydrogens decreases in the order of M = Cr > W > Mo.     

CH4, CO2和H2O在非金属原子修饰石墨烯表面的吸附

煤层气(矿井瓦斯)是一种有望替代传统化石燃料，如煤、石油和天然气的非常规气体. 作为可得的清洁能源，它的利用被认为是节能和经济的选择. 在本工作中，非金属原子X(X=H，O，N，S，P，Si，F，Cl)修饰的石墨烯(Gr)被用来代表具有结构异性的煤表面模型. 通过密度泛函理论系统地研究了煤层气组分Y(Y=CH₄，CO₂，H₂O)在非金属原子修饰石墨烯上的吸附作用. 结果表明Y在非金属原子修饰石墨烯上的吸附均为物理吸附. 态密度和差分电荷密度共同表明了这种弱的相互作用.其中，H和Cl对CH₄的作用较大； N、O、F、Cl对CO₂的作用较强； N，Cl对H₂O的影响不容忽视. 总的来说，吸附能大小依次为：H₂O>CO₂>CH₄. 因此，在CH₄富集的煤层里注入H₂O或CO₂可以与CH₄形成竞争吸附，进而提高煤层气采收率. 本工作提供了在分子水平下煤层气与非金属原子修饰石墨烯之间的相互作用的详情，并为煤层瓦斯的开采与分离提供了有用的信息.     

Theoretical Study on the Antioxidant Activity of Curcumin

The computational results for curcumin at the B3LYP/6-31G(d,p) level show that the enol form of curcumin is more stable than the diketo form because of an intramolecular hydrogen bond, which extends the conjugation effect in the enol chain, formed in the enol structure. Cis-diketone form can not be obtained, presumably due to the strong repulsion between the carbonyl dipoles aligned in parallel. According to the phenolic O-H bond dissociation enthalpy, curcumin in its most stable form can be suggested to be a relatively good antioxidant. In order to avoid overcoming H-bond interaction and to improve the antioxidant activity of curcumin, a catechol moiety was incorporated into curcumin for designing a novel antioxidant. It is found that the designed molecule is much more efficient to scavenge radical than curcumin, comparable to vitamin E. Moreover, the ionization potential of the designed molecule is similar to that of curcumin, indicating that the designed molecule can not display the prooxidant effect.     

Ring currents as probes of the aromaticity of inorganic monocycles : P5-, As5-, S2N2, S3N3-, S4N3+, S4N42+, S5N5+, S42+ and Se42+

Current-density maps were calculated by the ipsocentric CTOCD-DZ/6-311G** (CTOCD-DZ=continuous transformation of origin of current density-diamagnetic zero) approach for three sets of inorganic monocycles: S(4) (2+), Se(4) (2+), S(2)N(2), P(5) (-) and As(5) (-) with 6 pi electrons; S(3)N(3) (-), S(4)N(3) (+) and S(4)N(4) (2+) with 10 pi electrons; and S(5)N(5) (+) with 14 pi electrons. Ipsocentric orbital analysis was used to partition the currents into contributions from small groups of active electrons and to interpret the contributions in terms of symmetry- and energy-based selection rules. All nine systems were found to support diatropic pi currents, reinforced by sigma circulations in P(5) (-), As(5) (-), S(3)N(3) (-), S(4)N(3) (+), S(4)N(4) (2+) and S(5)N(5) (+), but opposed by them in S(4) (2+), Se(4) (2+) and S(2)N(2). The opposition of pi and sigma effects in the four-membered rings is compatible with height profiles of calculated NICS (nucleus-independent chemical shifts).     

环状芴基张力半导体拉曼光谱理论与实验研究

环状芴基张力半导体由于其特殊的分子结构，发射状排布的p轨道和纳米级空腔等诸多特点，引起了科学家广泛的关注.相对于直链型芴基半导体，环状芴基张力半导体展现出独特的光电性质.然而，迄今为止其振动性质没有被报道.对四元环芴的晶体与直链四聚芴粉末样品进行拉曼光谱表征和归一化处理，并结合理论计算.结果表明，与直链寡聚芴相比，环芴类似于碳纳米管的G峰发生了偏移，并且低频区域拉曼频移峰的峰强增加.其原因是由于张力的引入，改变了芴基主链的骨架和电子结构，加强芴骨架上π电子离域，同时使环芴中每个芴单元都参与到振动中.该研究结果为芴基张力半导体材料拉曼光谱的研究提供了一定的工作基础.     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

Sandwich-type transition metal complexes [(CBO)n]2M with carbon boronyl ligands (CBO)n (n=4–6)

A density functional theory investigation on a series of sandwich-type transition metal complexes [(CBO)_n]₂M (n=4–6; M=transition metals) with carbon boronyls (CBO)_n as effective aromatic ligands has been presented in this work at B3LYP level. The ground-states of these complexes possess staggered D_nd symmetries, while the corresponding eclipsed D_nh structures exist as transition states with slightly higher energies (within 5.8 kJ/mol). Carbon boronyl complexes [(CBO)_n]₂M are confirmed to be much more stable than their boron carbonyl isomers [(BCO)_n]₂M, which, on the other hand, take eclipsed ground-states with D_nh symmetries. The carbon boronyl complexes [(BCO)_n]₂M proposed in this work parallelize the well-known sandwich-type hydrocarbon complexes [C_nH_n]₂M in coordination chemistry with boronyl groups –BO isolobal to –H atoms in corresponding ligands.     

A kinetic stability study of <Emphasis Type="Italic">M</Emphasis>N<Subscript>5</Subscript> (<Emphasis Type="Italic">M</Emphasis>=Li,Na, K,and Rb)

A structure and kinetic stability study on some complexes with the general formula MN₅, where M are the alkali-metal atoms, Li, Na, K, and Rb, has been carried by using hybrid density functional methods. Complex B (C_2v) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Pyramidal structures A (C_5v) are kinetically unstable and they rapidly rearrange to the most stable planar structures B. At the QCISD(T)/6-311 + G*//B3LYP/6-311 + G* + ZPE (B3LYP/6-311 + G*) level, the decomposition barrier heights of LiN₅-B, NaN₅–B, KN₅-B, and RbN₅-B are predicted to be 19.9, 22.0, 22.5, and 23.0 kcal/mol, respectively. In addition, the rate constants of the decomposition reaction MN₅-B MN₃ + N₂ (M + Li, Na, K, and Rb) are also predicted using conventional transition state theory and canonical variational transition state theory, respectively.