Progress in crystal structure prediction

The results of the application of a density functional theory method incorporating dispersive corrections in the 2010 crystal structure prediction blind test are reported. The method correctly predicted four out of the six experimental structures. Three of the four correct predictions were found to have the lowest lattice energy of any crystal structure for that molecule. The experimental crystal structures for all six compounds were found during the structure generation phase of the simulations, indicating that the tailor-made force fields used for screening structures were valid and that the structure generation engine, which combines a Monte Carlo parallel tempering algorithm with an efficient lattice energy minimiser, was working effectively. For the three compounds for which the experimental crystal structures did not correspond to the lowest energy structures found, the method for calculating the lattice energy needs to be further refined or there may be other polymorphs that have not yet been found experimentally.     

Crystal Structure and Density Functional Theory Studies of （p-Methoxyphenyl） Thiosemicarbazide

1 INTRODUCTION Recently, the discoveries of antitumor effects ofinorganic complexes, especially of metal complexes,and their applications for curing cancer diseaseshave received increasing attention[1]. As a ligandwith potential S and N donors, thiosem…     

黄酮类化合物的密度泛函理论研究

在混合密度泛函B3LYP理论下,用6-31G*基函数研究了几种典型黄酮类化合物分子的几何结构、电子结构和分子的静电势,讨论了电子结构和分子活性部位的关系.     

Crystal Structure Prediction and Isostructurality of Three Small Molecules

A crystal structure prediction (CSP) study of three small, rigid and structurally related organic compounds (differing only in the position and number of methyl groups) is presented. A tailor‐made force field (TMFF; a non‐transferable force field specific for each molecule) was constructed with the aid of a dispersion‐corrected density functional theory method (the hybrid method). Parameters for all energy terms in each TMFF were fitted to reference data generated by the hybrid method. Each force field was then employed during structure generation. The experimentally observed crystal structures of two of the three molecules were found as the most stable crystal packings in the lists of their force‐field‐optimised structures. A number of the most stable crystal structures were re‐optimised with the hybrid method. One experimental crystal structure was still calculated to be the most stable structure, whereas for another compound the experimental structure became the third most stable structure according to the hybrid method. For the third molecule, the experimentally observed polymorph, which was found to be the fourth most stable form using its TMFF, became the second most stable form. Good geometrical agreements were observed between the experimental structures and those calculated by both methods. The average structural deviation achieved by the TMFFs was almost twice that obtained with the hybrid method. The TMFF approach was extended by exploring the accuracy of a more general TMFF (GTMFF), which involved fitting the force‐field parameters to the reference data for all three molecules simultaneously. This GTMFF was slightly less accurate than the individual TMFFs but still of sufficient accuracy to be used in CSP. A study of the isostructural relationships between these molecules and their crystal lattices revealed a potential polymorph of one of the compounds that has not been observed experimentally and that may be accessible in a thorough polymorph screen, through seeding, or through the use of a suitable tailor‐made additive.     

戊唑醇的分子结构、理论计算及热力学性质研究

在甲苯溶剂中利用缓慢蒸发法得到1-(4-氯苯基)-4,4-二甲基-3-(1H-1,2,4-三唑基甲基)戊醇-3（戊唑醇）的单晶,通过 X射线单晶结构分析法测定其晶体结构,晶体属单斜晶系,空间群为P2(1)/c,晶胞参数为：a = 1.1645(1) nm,b = 1.6768(2) nm,c = 1.7478(2) nm,β= 92.055(2),Dcalc.= 1.199 g/cm3,Z = 4,F(000)= 264。运用密度泛函理论 (DFT) B3LYP得到其优化几何构型并得到其频率。计算得到的结构参数与相应的实验值十分接近。运用微热量仪对标题物进行比热容测定,在所测温度范围283~353 K内,比热容随温度呈稳定的线性变化,根据测定的比热容方程,计算出戊唑醇以298.15 K为基础在283~353 K温区的的热力学函数：焓、熵和吉布斯自由能。     

Structure and vibrational spectra of dicyclopentadienylzinc. A DFT study

The quantum-chemical DFT calculations of the Cp₂Zn structure confirm the conclusion made earlier from the vibrational spectra that the sandwich structure (⁵-C₅H₅)₂Zn (A) is not energetically favorable and more favorable are the close in energy -structure (⁵-C₅H₅)(¹-C₅H₅)Zn (B) and -structure (¹-C₅H₅)₂Zn (C). The vibrational spectra of structures B and C with the DFT-derived force fields were calculated. A comparison of the calculated spectra of the isolated Cp₂Zn molecules with the experimental data gives no way of deciding between the B and C structures. It is most likely that the molecule is nonrigid and experiences a strong influence from the nearest environment in solution or in the crystalline state.     

Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br)

1‐(Chloromethyl)‐3‐nitrobenzene, C₇H₆NClO₂, and 1‐(bromomethyl)‐3‐nitrobenzene, C₇H₆NBrO₂, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In‐house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in‐house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.     

基于2,4-氧基双(苯甲酸)和含氮配体的四种过渡金属配合物的合成、结构与性能

采用水热法合成了4种过渡金属配合物{[Mn(2,4-Hoba)_2(bipy)(H_2O)_2]·2H_2O}_n(1),[Mn(2,4-oba)(phen)]n(2),[Co (2,4-oba)(bimyb)_(0.5)]n(3)和[Ni(2,4-oba)(bimyb)_(0.5)]_n(4)(2,4-H2oba=2,4-氧基双(苯甲酸),bipy=4,4′-联吡啶,phen=1,10-菲咯啉,bimyb=1,4-双(咪唑-1-甲基)苯),并用X射线单晶衍射、热重分析、红外光谱和元素分析等手段对其进行了表征。单晶结构表明:配合物1是一维链状结构,通过O-H…O氢键扩展为二维超分子结构。配合物2是一维波浪链状结构,通过芳香环π-π堆积作用扩展为二维波状网络结构。配合物3和4是由配体桥联双核桨轮单元产生的二维层状结构。此外,对配合物2～4的磁性进行了研究,磁交换耦合常数分别为-0.79、-8.97和-11.42 cm-1。根据配合物2～4的晶体结构,利用DFT-BS方法对配合物2～4的磁耦合行为进行了研究。结果表明,计算的交换耦合常数J与实验数据吻合较好。     

Synthesis and Theoretical Investigation of a New Hybrid Polymeric Iodoplumbate Based on Co-template： [（ipq）2（pea）（Pb3I9）·DMF]n

A new iodiplumbate polymer [（ipq）2（pea）（Pb3I9）-DMF]n 1 （ipq = N-（isopentyl）- quinolinium, pea = protonated ethylamine） was synthesized by self-assembly reaction of ipq·I, PbI2 with ethylamine and structurally characterized. 1 crystallizes in the triclinic system, space group P1 with α= 1.0731（4）, b = 1.2560（4）, c = 2.0785（7） nm, α = 96.378（5）, β= 91.132（2）, γ= 100.303（5）°, V= 2.7369（16） nm^3, Z= 2, Dc = 2.770 g/cm^3,μ = 14.307 mm^-1, F（000） = 2014, R = 0.0588 and wR = 0.1345. 1 features its hybrid structure concertedly templated by two kinds of organic cations, which exhibits interesting semiconductor property. In 1, the [Pb2I6]^2 n infinite chains shape the sketch of the title compound constructed from face-sharing of ideal and distorted PbI6 octahedra. Based on the crystal structure data, quantum chemistry calculation with DFT was used to reveal the electronic structure of 1.     

Preparation,Crystal Structure and Density Functional Theory Calculations of the Ion-pair Compound [Cl2Bz（3-MeQl）]（TCNQ）

A novel compound [Cl2Bz(3-MeQl) ](TCNQ) ([Cl2Bz(3-MeQl) ]+ = 1-(3,4-dichlo-robenzyl) 3-methlquinoline cation,TCNQ-= 7,7,8,8-tetracyanoquinodimethanide anion) has been synthesized by the reaction of [Cl2Bz(3-MeQl) ]Br and LiTCNQ,and its structure was determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic,space group P21/c. The structure analysis shows that the anions are stacked into a column with isolated π-dimers,and there is one type of TCNQ entries(TCNQ) ,in agreement with the IR spectra analysis and density functional theory calculations of the compound. The most prominent structural features are the completely segregated stacking columns of the TCNQ- anions and [Cl2Bz(3-MeQl)]+ cations.     

苯乙烯基吡啶类化合物几何结构与光谱的理论研究

采用量子化学密度泛函理论(DFT)方法分别在B3LYP/6-31G*, 6-31G**, 6-31＋G*水平上对苯乙烯基吡啶类化合物进行计算研究. 通过在相同水平下的振动频率分析发现苯乙烯基吡啶类化合物具有C₁对称性, 酯基的碳氧原子与苯环形成不同的离域大π键, 空间位阻和共轭效应使得两苯环处于两个不同平面, 二面角在60°与62°之间. 使用含时密度泛函理论(TD-DFT)方法计算第一激发态的电子垂直跃迁能, 得到最大吸收波长λ_max. 计算结果表明末端烷基链的长度对该类化合物的几何结构与振动光谱、电子光谱无影响.     

磷化镍晶体结构的密度泛函理论研究

运用密度泛函理论系统地研究了已知的磷化镍晶体如Ni3P、 Ni12P5、 Ni2P、 Ni5P4、 NiP、 NiP2 和 NiP3等的结构、成键以及相关的热力学稳定性,对于结构简易化合物（Ni2P和NiP3）的弹性行为进行了预测。这些数据有助于更好的理解磷化镍的催化活性。     

密度泛函理论方法研究双核铜化合物的磁性和自旋密度分布

Magnetic coupling constants J between Cu ions and spin density map for a binuclear complex Cu₂(2,2′-bpy)₂(4,4′-bpy)₂L₂ have been calculated by the combination of the broken symmetry approach with the spin project method under the DFT framework and the effect of nonorthogonality between magnetic α and β orbitals in the broken symmetry solution. The result indicates that using SV/SVP basis sets in the calculation of Gaussian 98 is much better than using LanL2DZ pseudo-potential function in above system. It is interesting that calculated J value is quite near to the experimental value in the studies of magnetic susceptibility.