Ionization energy reductions in small 2,5-dihydroxybenzoic acid-proline clusters

The photoionization of (pro)(n)DHB (pro = proline, DHB = 2,5-dihydroxybenzoic acid, n = 0, 1, 2 or 4) clusters was studied both experimentally and computationally. Experimentally the (pro)(n)DHB clusters are generated in the gas phase by laser desorption and supersonic jet entrainment. The photoionization thresholds are then determined by the mass-selective measurement of both one- and two-color photoionization efficiency curves. These experiments demonstrate that the ionization energies (IEs) of the (pro)(n)DHB clusters are substantially reduced in comparison with the IE of free DHB. Computational studies of the (pro)(n)DHB clusters provide insights into the mechanism of IE reduction. For the (pro)DHB system the IE reduction results from spin delocalization in the ion state of the cluster. In contrast, for the (pro)(2)DHB and (pro)(4)DHB clusters the IE reduction results from an inductive delocalization of electron density from pro to DHB in the ground state of the cluster. This latter effect, which is a result of the specific hydrogen-bonding interactions occurring in the mixed clusters, leads to IE reductions of >1 eV. Finally, determination of the energetics of the (pro)(2)DHB radical cation demonstrate that the DHB-to-proline proton transfer reaction is a barrierless, exoergic process in the ion state and that energetic demands for cluster dissociation to protonated (pro)(2) plus a deprotonated DHB radical are substantially lower than those for cluster dissociation to (pro)(2) plus DHB(+*). Cumulatively, these studies provide new energetic and mechanistic insights into both primary and secondary MALDI ionization processes.     

A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.     

ESI‐QTof‐MS characterization of hirsutinolide and glaucolide sesquiterpene lactones: Fragmentation mechanisms and differentiation based on Na+/H+ adducts interactions in complex mixture

Sesquiterpene lactones (SL) have been reported with various biological effects. Among the described SL skeletons, hirsutinolide and glaucolide have not been extensively studied by mass spectrometry (MS), especially how to distinguish them in organic matrices. Thus, this paper reports (1) a strategy of their differentiation based on MS behavior during the ionization and (2) a proposal of the fragmentation pattern for both SL‐subtypes. ESI(+)‐HRMS data of four isolated SL (hirsutinolides 1 and 3 ; glaucolides 2 and 4 ) were recorded by direct and UPLC water‐sample combined injections. These analyses revealed that hirsutinolides and glaucolides formed [M+Na]⁺ ion during the operation of the direct MS injection, and ([M+Na]⁺ and [M+H‐H₂O]⁺) and [M+H]⁺ ions were respectively observed for hirsutinolides and glaucolides during the operation of combined UPLC water and sample MS injection. Computational simulations showed that the complex hirsutinolide ( 1 )‐Na⁺ formed with a lower preparation energy compared with the complex glaucolide ( 2 )‐Na⁺. However, despite their different behavior during the ionization process, ESI(+)‐HRMS/MS analyses of 1 ‐ 4 gave similar fragmentation patterns at m/z 277, 259, 241, and 231 that can be used as diagnostic ions for both skeletons. Moreover, the differentiation strategy based on the nature of the complex SL‐adducts and their MS/MS fragmentation pattern were successfully applied for the chemical characterization of the extract from Vernonanthura tweedieana using UPLC‐ESI‐HRMS/MS. Among the characterized metabolites, SL with hirsutinolide and glaucolide skeletons showed the aforementioned diagnostic fragments and an ionization behavior that was similar to those observed during the water‐sample combined injection.     

Reachable and controllable sets for two-dimensional,linear, discrete-time systems

We consider two-dimensional discrete-time linear systems with constrained controls. We propose a simple polynomial time procedure to give an exact external representation of theN-step reachable set and controllable set. The bounding hyperplanes are explicitly derived in terms of the data of the problem. By using a result in computational geometry, all the calculations are made in polynomial time in contrast to classical methods. The limit case asN is also investigated.     

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.     

基于改进NAS-RIF的三维显微图像盲复原

对二维NAS-RIF算法进行了改进,并将它用于三维显微图像复原,分别用模拟样本和真实生物样本进行了实验。针对原算法对噪声有放大作用,提出了基于中值滤波去噪的改进。在支持域的确定、最小点的搜索上进行改进,提高复原质量。改进了原算法仅适用于均匀背景的不足,扩大了应用范围。实验结果表明,该算法在三维显微图像盲复原中具有较好的效果。     

用方阵乘幂求和法求线性方程组的数值解

介绍了一种新型的,不同于传统的雅克比或高斯塞德尔迭代法的,求解线性方程组的方阵乘幂求和法,并引入了方阵意义上求积分的龙贝格法.该算法成立须以方阵A为实阵,非奇异且主对角元素占优.该法较雅克比或高斯塞德尔迭代的计算量小,特别有助于求解大型线性方程组的问题.     

求解Euler方程的区域分解方法与并行算法

将复杂形状区域划分成多块子区域,研究发展了一种多块区域之间迎风守恒型的内边界耦合方法,实现相邻子区域解的光滑过渡,使多区耦合得到总体流场的数值解。对二维翼型跨音速流动和圆弧形隆起物超音速流动等进行了分区数值计算,并将计算结果与单区计算结果和实验结果作了比较。并行分区计算引入"先进先出"的同步控制等待机制,实现了高效率并行计算,还分析了影响并行效率的主要因素。     

单向悬挂屋盖结构的风致气弹耦合效应数值模拟

综合运用计算流体力学和计算结构力学技术,建立了适用于索膜结构流固耦合风振分析的CFD数值模拟方法,并编制了相应的有限元计算程序。应用该程序对具有不同参数的大跨度单向屋盖结构进行了风振响应分析,探讨了来流风速、屋面质量和初始预张力等参数对结构流固耦合特性的影响。研究表明,由于屋盖前缘周期脱落的大尺度旋涡是诱导结构振动的主要原因,随着大尺度旋涡沿屋面向下游移动,其动能逐渐转化为结构变形能,使结构振动形态呈现明显的涡激振动特征。屋面质量、来流风速和初始预张力是影响结构流固耦合性能的主要参数。对于索膜结构,仅通过刚性模型来确定结构风压并进行风振响应分析,其结果是不可靠的。