Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm

The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high‐dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT‐identified pathways can be used as valuable input guesses for double‐ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

宽离子能量检测范围垂直引入反射式飞行时间质谱仪的研制

本实验室研制了国内首台宽离子能量检测范围飞行时间质谱仪。仪器采用紧凑式电子轰击源设计,配合离子透镜系统有效的调制离子流,飞行时间质量分析器采用了离子垂直引入式,双场加速和双场反射以及大尺寸MCP检测装置设计。仪器单离子信号半峰宽约2 ns,仪器分辨率优于1600FWHM,检测实际样品质量范围为1~127 amu(仪器理论质量检测上限优于800 amu),可检测离子能量范围优于2个数量级(3~140 eV)。若该TOF质量分析器与短瞬高压脉冲放电离子源耦合联用,可广泛应用于高能离子束的快速检测,如真空阴极放电对制备薄膜、离子注入材料的表征,导电材料的离子电荷态分布以及离子扩散速度的测定等。     

聚苯并双噁唑酰亚胺的热分解动力学研究

采用二步法合成了以2,6-二(对-氨基苯)苯[1,2-d;5,4-d’]二噁唑和1,4-二(3,4-二苯氧基)苯四甲酸二酐(HQDPA)为单体的聚苯并双噁唑酰亚胺.该聚酰亚胺的预聚体聚酰胺酸的黏度为1.70 dL/g,经过热环化后能够生成浅黄色的聚酰亚胺薄膜.通过热重分析法研究了聚苯并双噁唑酰亚胺在N2气氛中的热降解机理.采用Flynn-Wall-Ozawa和Friedman法计算了聚苯并双噁唑酰亚胺热降解表观活化能,分别为356.36kJ/mol和370.54 kJ/mol,平均值为363.45 kJ/mol;反应级数为4.22,指前因子为6.44×1016s-1.采用Coast-Redfern法和Phadnis-Deshpande法研究了聚苯并双噁唑酰亚胺的热降解固相反应机理,认为该聚酰亚胺的热降解机理属于反曲线(A3)机理,是成核和增长模式(Avrami equation 2方程)控制的热降解反应,积分形式为g(X)=[-ln(1-X)]3.     

Use of the Bell–Evans–Polanyi Principle to predict regioselectivity of nucleophilic aromatic photosubstitution reactions

Regioselectivity of nucleophilic aromatic photosubstitution has been shown experimentally to depend upon activation energies of the competing transition states. Computational means of determining relative activation energies were sought, therefore, in order to predict regioselectivity. Optimization of the three triplet transition states of 2-chloro-4-nitroanisole with hydroxide ion gave energies of insufficient accuracy to predict regioselectivity. Computed enthalpy changes from the first triplet transition state to the triplet σ-complexes correlated precisely with the experimental activation energies. This exemplifies the Bell–Evans–Polanyi Principle, and it provides an accurate means of assessing regioselectivity.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles

After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.     

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. ¹H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on ¹³C and ¹⁵N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on ¹³C chemical shifts are investigated as a possible means of estimating hydrogen bond energies.     

DFT study of the electronic and charge transfer properties of perfluoroarene–thiophene oligomers

The ground state structures of 5,5″-diperfluorophenyl-2,2′:5′,2″:5″,2‴-quaterthiophene (1), 5,5′-bis{1-[4-(thien-2-yl)perfluorophenyl]}-2,2′-dithiophene (2), 4,4′-bis[5-(2,2′-dithiophenyl)]-perfluorobiphenyl (3), 5,5″-diperfluorophenyl-2,2′:5′,2″-tertthiophene (4), 5,5′-diperfluorophenyl-2,2′-dihiophene (5), and 5,5-diperfluorophenylthiophene (6) have been optimized at the B3LYP/6-31G(d), B3LYP/6-31G(d,p), PBE0/6-31G(d), and PBE0/6-31G(d,p) level of theories. The B3LYP/6-31+G(d) and PBE0/6-31+G(d) level of theories have been applied to investigate the absorption spectra. The PBE0 functional is good to predict the C–S bond lengths while the C–F bond lengths are good envisaged with B3LYP functional. The increment of thiophene rings between two perfluoroarene rings leads to red shift in absorption spectra. The electron affinities are energetically destabilized while energetic stabilization of the radical-cation increases by decreasing the thiophene rings from four to one. The perfluoroarene rings leads to enhance the electron injection.