改进的紧束缚势蒙特卡罗方法及其在碳纳米豆荚中的应用

提出了改进的紧束缚势蒙特卡罗方法, 通过减少计算紧束缚势能的原子数目, 大大缩短了模拟计算时间. 对平行纳米管联结的模拟测试结果表明, 与原方法相比, 改进方法的计算效率得到很大提高. 将该方法成功地用于对大体系碳纳米豆荚的模拟研究, 结果表明, 在单壁碳纳米管内部, 相对球面上存在空缺的富勒烯在2000 K左右的温度下可以相互联结, 否则, 只有在4500 K左右的高温下才能观测到富勒烯之间的联结; 富勒烯在管中的相互取向对最终结果影响不大.     

硅锗混合团簇GemSin(m+n≤10)的非正交紧束缚模型研究

Menon等[1]提出的非正交紧束缚模型(以下简称M-S NTB模型), 是基于s及p轨道的成键特征, 考虑了sp3杂化轨道间的非正交性对成键的贡献, 将计算量置于常规计算手段可接受的范围之内, 更适合于对碳族元素如C60[2], Sin[3]及Gen[4]等微团簇的研究. 这些工作表明, M-S NTB法是一种可信度较高、 计算量适中的半经验方法.     

C60分子的非线性元激发和电子能谱

1 计算方法在本文中我们利用推广的SSH 模型,采用自洽迭代的数值计算方法,得到C_(60)分子基态、激发态的电子能谱和几何结构.这与分子轨道和密度泛函理论的计算结果是极相符的.在研究导电聚合物,特别是trans-polyacetylene 链的电子态时,苏武沛等提出了著名的SSH 模型,从理论上阐明了非线性元激发(孤子、极化子、双极化子)的物理图象.鉴于C_(60)分子与PA 链有某些相似之处,实验证实了C_(60)分子中的每个C 原子,通过三个σ电     

化学教学中的模型方法及其应用

化学模型方法在化学教材和教学中有着广泛应用。本文对化学模型方法的含义、特征、条件及分类做了简要讨论。指出自觉认识和充分掌握这种科学方法的重要性和必要性,并提出运用中应注意的几个问题。     

ChemWindow 6.0在3D分子模型绘制中的应用

主要介绍了如何使用ChemWindow 6.0中SymApps 6.0程序绘制三维分子模型,并结合具体实例,对SymApps 6.0的特点和功能进行了探讨。     

量子化学模型方法在机械力化学中的应用

机械力化学作为一种无需溶剂的绿色化学技术得到广泛关注。然而,机械力化学反应机制需要从原子和分子尺度上深入理解力诱导的化学反应。在过去的20年中,量子化学模型方法在机械力化学机理研究中得到广泛应用,高精度量化计算可得到外力下变形分子的几何结构、能量、过渡态等诸多性质。本文介绍了目前机械力化学领域的主流量子化学模型的基本原理,同时也关注了这些模型方法在软件上的具体实现,并借助典型的案例阐述了量子化学模型在解释机械力化学机理中的作用与价值。     

超分子化学在药物共晶中的应用

药物共晶是一种新兴的药物晶型, 一个给定的活性药物分子通过形成共晶, 一方面可以大大丰富其结晶形式, 另一方面可以改善其物化性质及临床疗效. 本文从超分子化学的角度对药物共晶进行了综述, 列举了一系列通过氢键超分子合成子进行药物共晶设计和制备的研究实例, 旨在促进超分子化学和药学的交叉融合.     

分子模型方法在色谱手性分离机理研究上的应用

介绍了计算机辅助的分子模型设计和理论计算方法,综述了近十年来该方法在液相色谱手性分离机理研究中的应用,主要集中在Ｐｉｒｋｌｅ类型和环糊精类型的手性固定相的研究上,随着计算机软件与硬件的发展,这种方法在手性识别机理研究中的应用会更加广泛。     

离子迁移质谱技术及其在脂质分析中的应用

脂质在细胞和生物组织中发挥着重要作用,传统的脂质组学分析方法虽可以实现脂质鉴定,但脂质结构的多样性和相似性仍为脂质组学研究中全脂质分析提出了巨大的挑战。离子迁移谱是根据离子在缓冲气体或电力场中的迁移特性对其进行分离的技术,将离子迁移谱与传统脂质分析方法联用不仅有助于复杂脂质的分离,同时还可对脂质异构体进行分析鉴定,提高脂质分析的分辨率和选择性。该文主要对不同离子迁移质谱技术及其在脂质分析中的应用进行综述,并对其未来发展方向进行了展望。     

Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules

The polaron might play an important role in the process of charge migration through duplex DNA stack. In the present work, we investigate properties of hole polarons in DNA molecules containing identical base pairs, such as poly(G)-poly(C) and poly(A)-poly(T), An extended tight-binding model (extended Su-Schrieffer-Heeger model), which involves the effect of an electric field in the direction of DNA stack, will be introduced. The transfer integral and electron-phonon coupling parameters in this model are obtained according to ab initio calculation for different base pair dimers. Calculations reveal that the polaron in poly(A)-poly(T) has a wider shape and a higher mobility under a specific electric field than that in poly(G)-poly(C) DNA stack.     

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.     

Electronic structures and long‐range electron transfer through DNA molecules

Quantum chemical calculation on an entire molecule of segments of native DNA was performed in an ab initio scheme with a simulated aqueous solution environment by overlapping dimer approximation and negative factor counting method. The hopping conductivity was worked out by random walk theory and compared with recent experiment. We conclude that electronic transport in native DNA molecules should be caused by hopping among different bases as well as phosphates and sugar rings. Bloch type transport through the delocalized molecular orbitals on the whole molecular system also takes part in the electronic transport, but should be much weaker than hopping. The complementary strand of the double helix could raise the hopping conductivity for more than 2 orders of magnitudes, while the phosphate and sugar ring backbone could increase the hopping conductivity through the base stacks for about 1 order of magnitude. DNA could transport electrons easily through the base stacks of its double helix but not its single strand. Therefore, the dominate factor that influences the electronic transfer through DNA molecules is the π stack itself instead of the backbone. The final conclusion is that DNA can function as a molecular wire in its double helix form with the conditions that it should be doped, the transfer should be a multistep hopping process, and the time period of the transfer should be comparable with that of an elementary chemical reaction. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 112–130, 2000     

Energy transfer processes in phycobilisome model complex at 77 K

Ultra time-resoived huorescence spectra were used to study the energy transter processes and mechanism of complex PEC/PC/APC at 77 K, which was reconstructed with phycobiliproteins (PEC, PC and APC) of Anabaena variabilis, and has intact light-harvesting system and single terminal emitter. The energy transfer relationships between different chromophores especially between rod and core were also discussed based on fluorescence decay kinetic under different detected wavelengths. As a result, we got the possible energy transfer pathways and transfer time constants to be 29 ps between two PEC trimers, 12 ps between PEC and C-PC, 51 ps between rod and core.     

Theoretical study of long range electron transfer in Phthalimide–Peptide–Methyl Aminoacetate Model molecules

Long-range electron transfer (ET) matrix elements (V_PS), rate constants (k_ET) and reorganization energies for ET from phthalimide radical (pha) moiety to methyl aminoacetate radical (aa) moiety in pa–(gly)_n = 0–6–aa (pa = C₆H₄(CO)₂N–(CH₂CO), gly = glycine, aa = HNCH₂COOCH₃) ionic molecules have been investigated using two-state variational method (TSVM) and classical rate model. Calculations on V_PS reveal that the overlap between the frontier orbitals of two diabatic states is quite small, which leads to a small value of V_PS. k_ET has a minimum at the range n = 1–3 for β-strand conformation, but linearly increases as the peptide chain length (n) increases for pro II-helix conformation. These results are in good agreement with the experimental predictions. Relevant ET mechanisms are elucidated. The transition energies for charge transfer in such systems are also calculated to test the influences of local dipoles on the potentials of the donor and acceptor. For comparison electron couplings in [pa–(gly)_n = 1,3–aa]⁺ cations are calculated and the effects of electron correlation on inner reorganization energies in pha + pha^−/+ self-exchange reactions are examined at different levels of theory respectively. Calculated results are discussed also.     

Contributions of the distance-dependent reorganization energy and proton-transfer to the hole-transfer process in DNA

A kinetic study of the single-step hole transfer in DNA was performed by measuring time-resolved transient absorption. DNA molecules with various sequences were designed and conjugated with naphthalimide (NI) and phenothiazine (PTZ) to investigate the sequence and distance dependence of the single-step hole transfer between guanines (Gs). Hole injection into DNA was accomplished by excitation of the NI site with a 355 nm laser pulse, and the kinetics of the hole-transfer process were investigated by monitoring the transient absorption of the PTZ radical cation (PTZ.+). Kinetic analysis of the time profile of PTZ.+ based on the kinetic model showed that the distance dependence of the hole-transfer process was significantly influenced by the DNA sequence. Results of temperature- and isotope-effect experiments demonstrated that the activation energy increased as the number of bridge bases separating the Gs increased. This is because of the distance-dependent reorganization energy and contribution of the proton-transfer process to the hole transfer in DNA.     

Bioluminescence resonance energy transfer from aequorin to a fluorophore: an artificial jellyfish for applications in multianalyte detection

In nature, the green light emission observed in the jellyfish Aequorea victoria is a result of a non-radiative energy transfer from the excited-state aequorin to the green fluorescent protein. In this work, we have modified the photoprotein aequorin by attaching selected fluorophores at a unique site on the protein. This will allow for in vitro transfer of bioluminescent energy from aequorin to the fluorophore thus creating an artificial jellyfish. The fluorophores are selected such that the excitation spectrum of the fluorophore overlaps with the emission spectrum of aequorin. By modifying aequorin with different fluorophores, bioluminescent labels with different emission maxima are produced, which will allow for the simultaneous detection of multiple analytes. By examining the X-ray crystal structure of the protein, four different sites for introduction of the unique cysteine residue were evaluated. Two fluorophores with differing emission maxima were attached individually to the mutants through the sulfhydryl group of the cysteine molecule. Two of the fluorophore-labeled mutants showed a peak corresponding to fluorophore emission thus indicating resonance energy transfer from aequorin to the fluorophore.     

A method for molecular correlation energy calculations. Application to the determination of dissociation energies of diatomic and polyatomic molecules

A simple and economical method for molecular correlation energy calculations is developed. In this method, the internal part of the correlation energy is calculated by means of a CI in a minimal basis set and the non-internal part (semi-internal and all-external) is evaluated using an original atoms-in-molecule method. It is successfully applied to the determination of dissociation energies of some diatomic (H₂, NH, C₂, CN, N₂, CO, NO, O₂, F₂) and polyatomic (H₂O, N₂O, CO₂, N₃H, CH₂N₂, CH₂CO, C₂N₂) molecules. The results are compared to those obtained using very elaborate variational methods.Aspirant du Fonds National Belge de la Recherche Scientifique.     

Thin-film voltammetry and its analytical applications: A review

Electrochemical reactions at the interfaces of immiscible electrolyte solutions (ITIES) are of fundamental importance in the fields of chemical, biological and pharmaceutical sciences. Four-electrode cell setup, scanning electrochemical microscopy (SECM) and thin-film voltammetry are the three most frequently used methods for studying the electrochemical processes at these interfaces. The principle, experimental design, advantages and challenges of the three methods are described and compared. The thin-film voltammetry is highlighted for its simplicity in experimental operation and kinetic data analysis. Its versatile analytical applications are discussed in detail, including the study of redox properties of hydrophobic compounds, evaluation of interfacial electron transfer kinetics, synthesis of nanoparticles/nanostructures, and illustration of cross-membrane ion transport phenomena.     

Two-phase model of hydrolysis kinetics and its applications to anaerobic degradation of particulate organic matter

The various equations of hydrolysis kinetics included into the generalized simulation model (METHANE) were tested on the anaerobic digestion of cellulose, sludge, and cattle manure. The good agreement between the model simulation results and experimental data was obtained. The Contois equation, taking into account a hydrolytic biomass, and the firstorder equation with respect to the particulate substrate only, were shown to be the approximations of two-phase hydrolysis kinetics.