Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/K = 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.     

NMR shielding constants of CuX,AgX, and AuX (X = F,Cl, Br,and I) investigated by density functional theory based on the Douglas–Kroll–Hess Hamiltonian

Two‐component relativistic density functional theory (DFT) with the second‐order Douglas–Kroll–Hess (DKH2) one‐electron Hamiltonian was applied to the calculation of nuclear magnetic resonance (NMR) shielding constant. Large basis set dependence was observed in the shielding constant of Xe atom. The DKH2‐DFT‐calculated shielding constants of I and Xe in HI, I₂, CuI, AgI, and XeF₂ agree well with those obtained by the four‐component relativistic theory and experiments. The Au NMR shielding constant in AuF is extremely more positive than in AuCl, AuBr, and AuI, as reported recently. This extremely positive shielding constant arises from the much larger Fermi contact (FC) term of AuF than in others. Interestingly, the absolute values of the paramagnetic and the FC terms are considerably larger in CuF and AuF than in others. The large paramagnetic term of AuF arises from the large d‐components in the Au d_π –F p_π and Au sd_σ–F p_σ molecular orbitals (MOs). The large FC term in AuF arises from the small energy difference between the Au sd_σ + F p_σ and Au sd_σ–F p_σ MOs. The second‐order magnetically relativistic effect, which is the effect of DKH2 magnetic operator, is important even in CuF. This effect considerably improves the overestimation of the spin‐orbit effect calculated by the Breit–Pauli magnetic operator. © 2013 Wiley Periodicals, Inc.     

Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

Structure and spectroscopic aspects of water‐halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods

In this article, we propose a stochastic search based method, namely genetic algorithm in conjunction with density functional theory to evaluate structures of water‐halide microclusters, with the halide ion being Cl^?, Br^?, and I^?. Once the structures are established, we evaluate the infrared spectroscopic modes, vertical detachment energies and natural population analysis based charges. We compare our results with available experimental and theoretical results. © 2012 Wiley Periodicals, Inc.     

Synthesis and Characterization of Functionalized Polyorganosiloxanes Containing Amino and Fluorocarbon Side Chains

A series of functional polyorganosiloxanes containing fluorocarbon side chain and amino groups had been synthesized by ring-opening polymerization. The raw materials used were Octamethyl cyclotetrasiloxane (D₄), dodecafluoroheptyl-propyl-trimethoxylsilane (502) and γ-aminopropyltriethoxylsilane (550), respectively. FTIR, ¹H-NMR, ¹³C-NMR, and ¹⁹F-NMR were used to characterize the copolymer structures. The surface properties of the functional polyorganosiloxanes emulsions were discussed. The results showed that the functional polyorganosiloxanes containing fluorocarbon and amino side chains had low surface tension and excellent water repellency.     

Swelling and Network Parameters of 1-Hexadecene-Co-Trimethylolpropane Distearate Monoacrylate Sorbers

Linear and crosslinked copolymers with different compositions of 1-hexadecene and trimethylolpropane distearate monoacrylate monomers were synthesized and evaluated for oil-absorbency application. Different concentrations of ethylene glycol diacrylate (EGDA) and ethylene glycol dimethacrylate (EGDMA) crosslinkers were used. The concentration of both crosslinkers was varied from 0.5% to 2%. Copolymer compositions were determined from ¹H NMR spectroscopy. Monomer reactivity ratios were calculated using Fineman-Ross and Kelen-Tudos techniques at low conversions. The oil absorbency and swelling rate constant were measured and influenced mainly by the degree of crosslinking and the hydrophobicity of copolymer units. The final equilibrium oil content, volume fraction of polymer and swelling capacity were determined at 298 K. The effective crosslinking density V_e, theoretical crosslink density V_t, the average molecular weight between the crosslinks M_c and the polymer-toluene interaction parameter χ were determined from swelling measurements. The efficiencies of EGDA and EGDMA crosslinking agents toward copolymers were determined.     

新型π-扩展TTF衍生物的合成、晶体结构及量子化学计算

以对苯二胺为起始原料合成了2个新型的π-扩展四硫富瓦烯(TTF)衍生物,即N,N’-2(4,5-二苄硫基-1,3-二硫杂环戊烯-2-叶立德)-苯-1,4-二胺(5a)和N,N’-2(4,5-二甲酯基-1,3-二硫杂环戊烯-2-叶立德)-苯-1,4-二胺(5b),并利用氢核磁共振(1H NMR)、质谱(MS)、傅里叶变换红外光谱(FTIR)和单晶X射线衍射(XRD)等方法对化合物结构进行了表征.晶体结构分析结果表明,化合物5a和5b分属三斜晶系、P1空间群和单斜晶系、P21/n空间群.化合物5a和5b均为非平面结构分子,分子中对苯二亚胺平面和1,3-二硫杂环平面形成的二面角分别为87.61°(5a)和43.77°(5b).运用Gaussian 09程序,采用密度泛函理论(DFT)方法在B3LYP/6-31+G(d,p)水平上进行了量子化学计算,对化合物的前线分子轨道、静电势和电子吸收光谱进行了讨论,计算结果与实验值基本一致.     

基于第一性原理方法研究ReOx在ReOx-Rh/ZrO2和ReOx-Ir/ZrO2催化的甘油氢解反应中的作用机制

采用密度泛函理论研究了ZrO₂负载的Ru基、Rh基以及Re改性的Rh基、Ir基催化剂上甘油氢解生成1,2-丙二醇和1,3-丙二醇的热力学过程, 重点考察了ReO_x调变催化剂活性和选择性的作用机制. 结果表明, Ru/ZrO₂和Rh/ZrO₂催化剂上甘油分解经由脱水-加氢反应途径, 1,2-丙二醇的生成是热力学有利过程, 其中Ru基催化剂活性更高. 在Re修饰的Rh基和Ir基催化剂上, 反应遵循直接氢解机理, 其中金属表面解离的氢原子进攻ReO_x团簇上与醇盐紧邻的C-O键是催化甘油转化为丙二醇最核心的步骤. ReO_x-Rh/ZrO₂催化剂上1,2-丙二醇为主要产物, 并伴随1,3-丙二醇的生成, ReO_x的修饰则显著提高了Ir/ZrO₂催化剂上1,3-丙二醇选择性. 与单金属催化剂上发生的间接氢解机理相比, 修饰催化剂上1,3-丙二醇选择性的提高可主要归因于Rh(Ir)-Re协同催化的直接氢解反应过程, 其中羟基化铼官能团有利于末端醇盐中间体的生成. ReO_x-Ir/ZrO₂催化剂上较大的Ir-Re团簇使得末端金属醇盐的立体优选性比次级醇盐更为突出, 从而具有最高的1,3-丙二醇选择性.     

Theoretical Study on the Structural and Optoelectronic Properties of the Linear Perfluorooctane Sulfonate （PFOS）

The perfluoroalkyl substances(PFS) have attracted considerable attention in recent years as a persistent global pollutant to be able to bioaccumulate in higher organisms.In this paper,theoretical analysis on electronic structures,optoelectronic properties and absorption spectra properties of the perflurooctane sulfonate(PFOS) in gas phase have been investigated by using the DFT/TD-DFT method.The geometric structures,electrostatic potentials,energy gaps,ionization potentials,electron affinities,frontier molecular orbital,excitation energies and absorption spectra for the ground state of PFOS were calculated.The result indicates that the ability of accepting electron of neutral PFOS is larger than that of anionic PFOS,while the electron excited by UV irradiation from HOMO to LUMO in the anionic PFOS is easier than that in the neutral PFOS.     

Bonding of Hydroxyl and Epoxy Groups on Graphene： Insights from Density Functional Calculations

Density functional theory and GGA-PW91 exchange correlation function were performed to simulate the bonding behavior of hydroxyl and epoxy groups on the graphene surface. We compared the different binding energies for two epoxy groups, as well as one hydroxyl group and one epoxy group on all possible positions within a 6-fold ring, respectively. The calculated results suggest that two oxygen-containing groups always tend to bind with the neighboring carbon atoms at the opposite sides. Moreover, two hydroxyl groups on the meta position are unstable, and one of the hydroxyl groups easily migrates to the para position. In contrast to the disperse arrangement, the aggregation of multiply hydroxyl groups largely enhances the binding energy of every hydroxyl group. It is worth noting that the binding sites and hydrogen bonds play an important role in stability. Our work further points out the number of oxygen-containing groups and the location of oxide region largely influence the electronic properties of graphene oxide.