生物分子计算进展*

由于生物分子在化学反应中具有高度的并行性和识别能力,使生物分子计算在解决组合优化问题中显示出巨大的优势。生物分子计算已成功地应用于计算哈密顿路径、最大集合以及逻辑运算中的SAT类问题等NP完全问题。本文总结了生物分子计算的基本思想与计算方法、生物分子计算的应用与进展,并对生物分子计算的发展趋势作了评述。     

溶剂化团簇银的制备及表征

报导了在O/W,W/O,W/O/W以及LC这些有序分子集合体中制备Ag胶体的研究成果.利用W/O/W和LC可实现用高浓度AgNO3与N2H4·H2O反应制备出10nm以下的稳定Ag粒及Ag胶体.采用紫外可见、X射线衍射、电子显微技术对胶体及银粒进行了表征.发现团簇Ag外有层状结构.通过分析指出,层状结构体现了表面活性剂、助表面活性剂的有序双分子包复.     

分子力学计算的参数化过程

介绍了如何通过设计模型分子构造参数的方法和过程：首先设计模型分子；在平衡位置附近选择几个点，对模型分子进行分子力学和量子化学的计算；计算出量子化学能量Eqm和分子力学能量Emm的差值；然后对结构参数（健长，键角，二面角）和能量差值进行拟合，得拟合曲线的方程，从方程的系数可求出参数．文章给出了一些实例．     

生物分子辅助溶剂热合成硫化锑纳米棒

以SbCl3和L-胱氨酸为反应原料,采用溶剂热法在170℃反应12h,制得硫化锑(Sb2S3)纳米棒.X射线衍射(XRD)、能量分散光谱(EDS)和X射线光电子能谱(XPS)研究表明所得产物为典型的Sb2S3正交结构.场发射扫描电子显微镜(FESEM)和透射电子显微镜(TEM)研究显示,Sb2S3纳米棒长为3～6μm,平均直径约为150nm.讨论了不同反应时间对Sb2S3的形成及其形貌的影响,并根据实验结果对所合成的一维纳米棒可能的形成机理进行了简单的探讨.     

溶剂化变色法测定有机分子β的若干问题

溶剂化变色法是测定有机分子超极化率．的一种半定量方法,已为许多实验室采用并取得了较好的结果．它的理论依据是描述有机分子产值的双能级模型【小式中：P。、11。分别为分子的基态和激发态偶极矩,。e。和11e。则分别为基态和激发态的跃迁频率和跃迁偶极矩．这包括三个方面     

分子束中生物分子的光谱与结构

研究分子束中的生物分子有助于探讨生物分子的固有性质和由于生物环境而引起的其他性质之间的区别。本文首先介绍了一种可将生物分子在气相中"孤立"的实验技术,即激光解吸并分子束冷却技术,同时还介绍了与该研究方向相关的光谱方法,即UV/UV和IR/UV烧孔光谱等。并回顾了近年来人们应用这些实验技术对分子束中的氨基酸和短肽、核酸碱基、糖类和神经递质类分子以及它们的团簇最新研究进展。文中还简要介绍了一种新的应用于构象异构动力学研究的光谱方法,即激励辐射泵浦-注孔(SEP-HF)和激励辐射泵浦-布居转移(SEP-PT)。最后,综述了短肽离子光解离动力学和短肽离子中发生的电荷快速转移动力学过程的研究进展。     

非平衡溶剂化的连续介质模型和超快过程溶剂效应

在连续介质理论基础上, 根据Jackson的能量积分公式导出非平衡态静电自由能和溶剂化能的正确表达式. 引入“弹簧能”概念, 对平衡态和非平衡态的静电能构成给出了合理解释, 即此能量由溶质自由电荷和溶剂极化电荷的自能、 两者之间的相互作用能和极化电荷的“弹簧能”构成. 对目前几种代表性的非平衡溶剂化理论进行了论证和比较, 指出其中存在的基本理论问题. 根据新的非平衡溶剂化能建立了电子转移反应溶剂重组能的双球模型、 光谱移动的单球孔穴点偶极模型, 多级展开方法和非平衡溶剂效应的数值解方法.在Poisson方程求解中引入类导体屏蔽模型, 建立了任意孔穴极化电荷数值解方法并应用到Closs-Miller电子转移体系, 得到与实验值吻合的溶剂重组能, 解决了传统非平衡溶剂化理论高估溶剂重组能的问题.     

1,4-二氧六环和氨分子氢键团簇的从头算

在不同基组水平上,对１,４－二氧六环和氨分子氢键团簇体系进行了从头算分子转道法研究,优化得到中性团簇,离子团簇和碎片离子（质子化团簇离子和非质子化团簇离子）平衡几何构型,研究结果表明：中性团簇最稳定构型为Ｒ－ＨＮ２－ＨＮＮ２（Ｒ：１,４－二氧六环）,离子团簇由于发生质子转移,其构型与中 团簇有较大的淡同,两类碎片离子Ｒ（ＮＨ３）＋和Ｒ（ＮＨ３）Ｈ＾＋与中性团簇Ｒ（ＮＨ３）的结构也有所不同     

N_2H_4-CH_3OH氢键团簇体系的从头计算

用从头计算法研究了 (N2 H4-CH3OH)氢键团簇体系。分别在HF/6 31G 和HF/6 31G 水平上对它们的中性和离子团簇进行几何全优化 ,得到了 3种中性混合团簇稳定构型和离子混合团簇稳定构型 ,并对其能量和稳定性进行了比较。讨论了 3种不同构型离子团簇可能的解离通道。给出了质子化混合团簇的稳定构型 ,并对其可能的解离通道进行了讨论。文中最后计算出N2 H4,CH3OH ,(N2 H4-CH3OH)团簇的质子亲和能 (PA) ,分别为 :2 0 6.7kcal/mol,1 78.3kcal/mol,2 2 7.5kcal/mol,其中质子亲和能PAcalc[N2 H4]与实验值PAexp[N2 H4]=2 0 4 .8kcal/mol符合得很好。     

聚乙烯单链松驰过程的分子模拟

利用分子模拟方法研究了不同链长聚乙烯单链折叠过程和相关的松弛和坍塌机理．发现在链长短于１０００ＣＨ２单元时,聚乙烯的链段主要通过整体塌缩机理进行折叠和取向;而链长超过１０００ＣＨ２单元时,可以明显地观察到局部取向团簇的形成,聚乙烯单链通过局部塌缩机理进行折叠和取向．通过对各阶段团簇数目,体系取向链段长度的表征,说明体系在模拟时间范围内表现了很强的松驰特性．     

Ultrafast Structural Dynamics of Biomolecules Examined by Multiple‐Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L ‐α‐glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal‐mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two‐dimensional infrared (2D IR) spectra, which are simulated using time‐domain third‐order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.     

Exploring the first-shell and second-shell structures arising in the microsolvation of Li+ by rare gases

An evolutionary algorithm was used to search for the low-energy structures of Li⁺Ar_n and Li⁺Kr_n (n = 1 − 14). Two functions were used to describe the interaction potential at the CCSD(T)/aug-cc-pVQZ level of theory: one is based on a sum of all pair potentials, whereas the other includes three-body interactions. In general, the global minimum structures are similar for both Li⁺Ar_n and Li⁺Kr_n. Modifications in the octahedral structure of the first solvation shell lead to a high-energy penalty. Conversely, the second solvation shell shows a panoply of minima with similar energies that are likely to be interconverted. Post-optimization at the MP2 level confirmed that, for n = 2 and 3, one has to include three-body terms in the potential to reproduce the low-energy structures. Additionally, MP2 calculations indicate that energy reorder of the global minimum structure observed for Li⁺Kr₈ is related to the Kr₃ Axilrod-Teller-Muto term included in the potential.     

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

The absorption properties of chromophores in biomolecular systems are subject to several fine‐tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point‐charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.     

A Theoretical Study of LiHe+ n , NaHe+ n , and MgHe+ n Complexes, with n=1, 2, 3, 4

The LiHe⁺ _n , the NaHe⁺ _n , and the MgHe⁺ _n complexes with n=1, 2, 3, 4 were studied using ab initio calculations with the MP2/6-311+G(3df, 3pd) method. The complexes are found to be stable. For the n=1 complexes, previous results were available and the calculations performed are in good agreement with those results. This lends credibility to the results obtained for the complexes with higher n.     

Homolytic versus Heterolytic Dissociation of Alkalimetal Halides: The Effect of Microsolvation

Herein we report density functional calculations of homolytic and heterolytic dissociation energies of the diatomic alkalimetal halides MX (M=Li, Na, K, Rb, and Cs and X=F, Cl, Br, I, and At) and their corresponding microsolvated structures MX?(H₂O)_n (n=1 to 4). Our results show that the homolytic dissociation energy of the MX?(H₂O)_n species increases with the number of water molecules involved in the microsolvated salts. On the other hand, the heterolytic dissociation energy follows exactly the opposite trend. As a result, while for the isolated diatomic alkalimetal halides, homolytic dissociation is always favored over heterolytic dissociation, the latter is preferred for CsF and CsCl already for n=2, and for n=4 it is the preferential mode of dissociation for more than half of the species studied.     

Electronic and Vibrational Spectroscopy of 1‐Methylthymine and its Water Clusters: The Dark State Survives Hydration

Electronic and vibrational gas phase spectra of 1‐methylthymine (1MT) and 1‐methyluracil (1MU) and their clusters with water are presented. Mass selective IR/UV double resonance spectra confirm the formation of pyrimidine‐water clusters and are compared to calculated vibrational spectra obtained from ab initio calculations. In contrast to Y. He, C. Wu, W. Kong; J. Phys. Chem. A, 2004 , 108, 94 we are able to detect 1MT/1MU and their water clusters via resonant two‐photon delayed ionization under careful control of the applied water‐vapor pressure. The long‐living dark electronic state of 1MT and 1MU detected by delayed ionization, survives hydration and the photostability of 1MT/1MU cannot be attributed solely to hydration. Oxygen coexpansions and crossed‐beam experiments indicate that the triplet state population is probably small compared to the ¹nπ* and/or hot electronic ground state population. Ab initio theory shows that solvation of 1MT by water does not lead to a substantial modification of the electronic relaxation and quenching of the ¹nπ* state. Relaxation pathways via ¹ππ*¹–nπ*¹ and ¹ππ *–S₀ conical intersections and barriers have been identified, but are not significantly altered by hydration.