The molecular dynamic study of anharmonic effects at Cu(111) and Ag(111) surfaces in the presence of Cu- and Ag-trimer island

The molecular dynamics (MD) technique based on semi-empirical potentials, is used to carry out the diffusion of Cu- and Ag-trimer on Cu- and Ag(111) surface at 300, 500 and 700 K temperatures. The constant energy MD simulation elaborates the anharmonic effects at the surface such as fissures, dislocations and vacancy creation, in the presence of island. The fissures and dislocations formed are in the range of 1.5–4 Å and 1–7 Å, respectively, from the island's position. The Cu and Ag islands both diffuse easily on Cu(111) surface, manipulate that the trend of diffusion is faster on Cu surface as compared to Ag surface. The process of breaking and opening of the island has also been observed. Moreover, a surface atom popped-up at 700 K by creating a vacancy near the Cu island on Ag surface. The rate of diffusion increases with the increase in temperature, both for homo- and hetero-cases.     

RNA synthesis via dimer and trimer phosphoramidite block coupling

The solid-phase synthesis of oligoribonucleotides using dimer and trimer phosphoramidite blocks is described. This method significantly reduces the total number of steps required in the synthesis of a target RNA sequence, provides more material, and simplifies separation of the product from shorter failure sequences. The procedure is illustrated by the synthesis of UpU, ApA, and UpUpU phosphoramidite blocks and their use in the rapid synthesis of oligoribonucleotides on a solid support. Dimer and trimer amidite blocks will likely find use in the large scale solution (or solid)-phase synthesis of siRNA drugs.     

大鼠金属硫蛋白晶体堆积形式的理论研究

考虑到蛋白质在结晶过程中溶液和晶体之间的动态平衡，蛋白质在溶液中的聚合状态决定了晶体堆积的最小单元。通过动态光散射实验以及计算机模拟，对大鼠金属硫蛋白亚型Ⅱ和兔肝金属硫蛋白亚型Ⅰ和Ⅱ的聚合物形式进行了比较，可以确定大鼠金属硫蛋白亚型Ⅱ在结晶条件下的缓冲液中应该以四聚体而不是二聚体形式存在。通过考察晶体的模型也可以发现，晶体的确可以通过四聚体的形式堆积得到，用四聚体堆积模型可以对晶体堆积作出更为合理的解释。     

Computational examination on monomeric,dimeric, trimeric structural and vibrational interactions,AIM, Hirshfeld,IGM and oxygenated solvent effect on optical properties for pyridine N-oxide

This work reports DFT (Density functional theory) and topological examination by means of AIM (Atom in molecule) theory, Laplacian electron density (ED), Electron –Localization function (ELF) and Hirshfeld surface were executed monomer, dimer and trimer structure of PNO molecule. These structures were optimized and Structural parameters like bond – length and Angles are compared by using B3LYP/6-311G++(d,p) basis set. Computed vibrational – frequencies and corresponding PED (Potential energy – Distribution) were also compared. Polarizability, Dipole moment and the electronic properties were calculated for all three cases of PNO molecule. Hirshfeld surface investigation has been executed to achieve the C–H?O/N–O?H type of hydrogen -bond intermolecular interactions. Moreover, Reactive site, inter/intra interactions are calculated, the optical behaviors for monomer structure of PNO were investigate by using UV–Vis spectroscopy in oxygenated solvents.     

光系统Ⅱ捕光复合物中能量传递动力学研究

采用时间分辩荧光光谱技术研究捕光色素复合体(LHCⅡ)荧光的时间光谱特性.以脉宽为120fs、重复率为82MHz、波长为360nm～420nm激光激发LHCⅡ样品荧光.原始信号经过数据处理,多指数拟合,解得了能量在LHCⅡ中传递的时间常量分别为320±10fs、4.0±0.1ps、20.0±0.1ps.相对应的各组分荧光占总荧光的百分比分别为3.4%、50%、46.6%.经过全局分析,解得荧光强度随波长变化曲线,其三个峰值波长分别为652nm、673nm、692nm(以去离子水为悬浮液)和658nm、687nm、700nm(以酒精为悬浮液).根据LHCⅡ结构以及荧光的时间、光谱特性分析,认为320±10fs的时间组分属于一个单体内同一膜平面中Chlb→Chla的能量传递时间;4.0±0.1ps的时间组分属于同一单体中不同膜平面间Chlb→Chla和Chla→Chla的能量传递时间;20.0±0.1ps的时间组分属于不同单体之间、不同三聚体之间Chla→Chla的能量传递时间.     

Synthesis and Structure of [Fe<Subscript>3</Subscript>O(O<Subscript>2</Subscript>CCH<Subscript>2</Subscript>OMe)<Subscript>6</Subscript>(H<Subscript>2</Subscript>O)<Subscript>3</Subscript>][FeCl<Subscript>4</Subscript>]

Abstract  The structure of [Fe₃O(O₂CCH₂OMe)₆(H₂O)₃][FeCl₄] · 2.5H₂O has been determined. The three iron atoms and the μ₃-oxo are coplanar. Each carboxylic ligand is bidentate and links two iron atoms in the cluster. The clusters are linked by intra-trimer hydrogen bonding to form a zigzag motif that forms sheets via hydrogen bonding involving disordered waters of hydration. The [FeCl₄]⁻ anion is intercalated between the hydrogen-bonded sheets. Crystal data: space group P2₁/n, a = 10.276(2), b = 22.793(5), c = 17.091(3) ?, β = 96.66(3)°, V = 3976(1) ?³, Z = 4, R = 0.0837, wR ₂ = 0.1836. Graphical Abstract  The structure of [Fe₃O(O₂CCH₂OMe)₆(H₂O)₃][FeCl₄] · 2.5H₂O has been determined in which the clusters are linked by intra-trimer hydrogen bonding to form a zigzag motif that forms sheets via hydrogen bonding involving disordered waters of hydration.      

Thermally induced oxidative trimerization of benzimidazole by copper(II) chloride in the solid state

Benzimidazolium trichlorocuprate(II) undergoes a redox reaction in the solid state at elevated temperature (∼240°C) to produce the cyclic trimer of benzimidazole and cuprous chloride. The trimer has been characterized by IR, NMR, and Mass spectroscopy. It has also been synthesized in lower yield by heating the mixtures of CuCl₂ and benzimidazole in different ratios or heating other compounds of CuCl₂ and benzimidazole. The absorption, emission, and excitation spectra of the trimer in two different solvents (TFA and DMSO) and a comparison of these results with those of benzimidazole are presented here.     

Dimers, trimers and oligomers of sulfur oxides: an ab initio and density functional study

Ab initio (HF/3-21G^*), DFT (B3LYP with basis sets 6-31G^*, 6-311+G^* and 6-311+G(2d)) and, in some cases, MP2/6-31G^* calculations, were done on cyclic dimers, trimers, etc. and on acyclic oligomers (with OH and H on the ends) of sulfur monoxide and sulfur dioxide. The four cyclic (SO)_n molecules were (S–O)₂ (1,3,2,4-dioxadithietane, 1a), (S–O)₃ (1,3,5,2,4,6-trioxatrithiane, 2a), (S(=O))₄ (tetrathietane 1,2,3,4-tetraoxide, 1b), and (S(=O))₆ (hexathiane 1,2,3,4,5,6-hexaoxide, 2b). The four cyclic (SO₂)_n molecules were the dioxide of 1a (1,3,2,4-dioxadithietane 2,4-dioxide, 1c), the trioxide of 2a (1,3,5,2,4,6-trioxatrithiane 2,4,6-trioxide, 2c), the tetraoxide of 1b (tetrathietane 1,1,2,2,3,3,4,4-octaoxide, 1d) and the hexaoxide of 2b (hexathiane 1,1,2,2,3,3,4,4,5,5,6,6-dodecaoxide, 2d). The 16 acyclic molecules (oxides of disulfane, trisulfane, etc. and oxides of oxadisulfane, dioxatrisulfane, etc.) were (–S–O–)_n, (–S(=O)–)_n, (–S(=O)O–)_n, and (–S(=O)₂–)_n, with n from 2 to 5 and HO, H at the ends. Most of these species are relative minima on the B3LYP/6-31G^* potential energy surface. In energy content, the SO dimer, etc. lie below, and the SO₂ dimer, etc. above, their SO_x components, at all the electron-correlated levels.     

Long-range magnetic ordering of S=1/2 linear trimers in A3Cu3(PO4)4 (A=Ca, Sr, and Pb)

Magnetic properties of S=1/2 linear trimer cluster compounds A₃Cu₃(PO₄)₄ (A=Ca, Sr, and Pb) were investigated. Magnetic susceptibility data for the three compounds showed that paramagnetic copper spins form trimers with the total spin of 1/2 below about 45 K. Specific heat and magnetization measurements indicated that the trimer clusters undergo ferromagnetic long-range ordering at for A=Ca and antiferromagnetic long-range ordering at for A=Sr and for A=Pb. A₃Cu₃(PO₄)₄ exhibited 1/3-magnetization plateau at least up to magnetic field of 55 T at 1.3 and 4.2 K. A₃Cu₃(PO₄)₄ with A=Sr and Pb showed a spin-flop transition near 0.03 T in the antiferromagnetic state at 0.08 K. Specific heat data at magnetic fields clearly showed broad maxima at low temperatures due to the finite intra-chain interaction in one-dimensional arrays of the trimers.     

Synthesis and photochromic reactivity of diarylethene trimers bridged by ethenyl and ethynyl unit

Two diarylethene trimers bridged by ethenyl and ethynyl groups were synthesized and their photochromic behaviors were examined. Upon irradiation of the trimers 2 and 4 with UV light, one-three photoinduced cyclization reactions occur. Each isomer was isolated and analyzed by ¹H NMR spectrum. The quantum yield of 2 and 4 is 0.52 and 0.311, respectively.