Predictability of the polymorphs of small organic compounds: crystal structure predictions of four benchmark blind test molecules

Predicting the crystal structure of an organic molecule from first principles has been a major challenge in physical chemistry. Recently, the application of Density Functional Theory including a dispersive energy correction (the DFT(d) method) has been shown to be a reliable method for predicting experimental structures based purely on their ranking according to lattice energy. Further validation results of the application of the DFT(d) method to four organic molecules are presented here. The compounds were targets (labelled molecule II, VI, VII and XI) in previous blind tests of crystal structure prediction, and their structures proved difficult to predict. However, this study shows that the DFT(d) approach is capable of predicting the solid state structures of these small molecules. For molecule VII, the most stable (rank 1) predicted crystal structure corresponds to the experimentally observed structure. For molecule VI, the rank 1, 2 and 3 predicted structures correspond to the three experimental polymorphs, forms I, III and II, respectively. For molecules II and XI, their rank 1 predicted structures are energetically more stable than those corresponding to the experimental crystal structures, and were not found amongst the structures submitted by the participants in the blind tests. The rank 1 structure of molecule II is predicted to exist under high pressure, whilst the rank 1 structure predicted for molecule XI has the same space group and hydrogen bonding pattern as observed in the crystal of 1-amino-1-methyl-cyclopropane, which is structurally related to molecule XI. The experimental crystal structure of molecule II corresponds to the rank 4 prediction, 0.8 kJ mol(-1) above the global minimum structure, and the experimental structure of molecule XI corresponds to the rank 2 prediction, 0.4 kJ mol(-1) above the global minimum.     

Ni2 分子的自旋极化效应

The density functional（B3P86）method has been used to optimize the structure of Ni2 molecule. Results show that the ground state for Ni2 molecule is 5 multiple state,not 1 multiple state and 3 multiple state the literatures concluded. That shows the spin polarization effect of Ni2 molecule of transition metal elements for the first time. They take 1 multiple state and 3 multiple state as the ground state of the Ni2 molecule because the minimal energy value of 1 multiple state,3 multiple state and 5 multiple state of Ni2 molecule are very close to each other. Meanwhile,we have not found out any spin pollution and the ground state wave function doesn't mingle with wave function with higher energy state. The result shows that the ground state for Ni2 molecule is 5 multiple state,which shows the spin polarization effect of Ni2 molecule of transition metal elements. That is,there exist 4 parallel spin electrons,at this time;the number of the non-conjugated electron is the most. These electrons occupy different spacious tracks so that the energy of Ni2 molecule reduces to the minimum. It shows that the effect of parallel spin of Ni2 molecule is larger than the effect of the conjugated molecule. It is obviously related to the effect of electron d delocalization. The Murrell-Sorbie potential function with the parameters for ground state for Ni2 molecule are also derived. Dissociation energy of the ground state Ni2 molecule is 1.835 eV,the equilibrium bond length is 0.2243 nm,and the vibration frequency is 262. 35 cm-1 . The force constants f2,f3 and f4 are 1.1901 aJ / nm2,-5.8723 aJ/nm3,21.2505 aJ/nm4 respectively.     

三维球状液晶的模型分子（C6H5）Si（OC6H4）3N结构的PM3研究

三维球状液晶的模型分子（Ｃ６Ｈ５）Ｓｉ（ＯＣ６Ｈ４）３Ｎ结构的ＰＭ３研究＊丁涪江张良辅（中国科学院成都有机化学研究所成都６１００４１）关键词三苯并硅杂烷环状分子ＰＭ３方法液晶分子多为棒状一维结构和盘状二维结构。最近发现三维球状液晶分子，即长链烷烃取代...     

新磺酰脲类化合物的合成、结构及构效关系研究(Ⅵ)1—N-〔2-(4-甲基)嘧啶基〕-2-甲酸甲酯-苄基磺酰脲的晶体及分子结构

合成了标题化合物 C6H4 (CO2 CH3 ) CH2 SO2 NHCONHC4 N2 H2 CH3 (C15H16N4 O5S,Mr=36 4 .38) ,用 X-射线晶体衍射法测定了其晶体结构。它属单斜晶系 ,空间群为P2 1/ c,a=10 .2 2 0 (1) ,b=9.938(1) ,c=17.2 4 6 (2 ) ,β=10 6 .2 6 (2 )°,V=16 81.6(3) 3 ,Z=4 ,Dc=1.4 39Mg/ m3 ,μ=0 .2 2 7mm-1,F (0 0 0 ) =76 0。结构由直接法解出 ,全矩阵最小二乘法修正 ,最终偏离因子 R=0 .0 4 98,w R=0 .132 7(I>2 σ(I) ) ,独立可观测点数为 3448。分子中的嘧啶磺酰脲、苯环及酯基分别形成 3个独立的平面共轭体系。     

Crystal structure analysis of the inclusion compound of 2′-hydroxy-2,4,4,7,4′-pentamethylflavan with 1,4-dioxan and water

The 2: 1: 2 complex of 2′-hydroxy-2,4,4,7,4′-pentamethylflavan (1) with 1,4-dioxan and water is triclinic, space groupP \(\bar 1\) , witha=8.164(1),b=8.960(1),c=14.644(1) Å, α=91.56(1), β=97.19(1), γ=103.37(1)°; there are two flavan host, two water molecules and a single 1,4-dioxan guest molecule in the unit cell. The dioxan molecule is linked,via a hydrogen-bonded water molecule, to the phenolic OH group. The second hydrogen of this water molecule is also involved in hydrogen bonding, in this case to the ring oxygen of a second host molecule. Thus a hydrogen-bonded hexameric unit, a common feature of many clathrates of phenolic hosts, is not found in the present structure.     

Geometric and excited-state properties of 1,4-bis(benzothiazolylvinyl)benzene interacting with 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] studied by a density-functional tight-binding method

The energetics and luminescent property of a guest molecule, 1,4-bis(benzothiazolylvinyl)benzene (BT), interacting with a host molecule, 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] (TPBI), in organic light-emitting diodes are studied by performing excited-state calculations using a time-dependent density-functional tight-binding method complemented with dispersion energy. It is found that the overlap between the TPBI emission and the BT absorption spectra shows an efficient energy transfer from the host molecule to the guest molecule when they are excited. The planar BT molecule becomes distorted when it is mixed with TPBI, resulting in a blue luminescence around 475 nm. The separation of the TPBI + BT mixture on a graphite surface is found to be energetically favorable, consistent with experimental observation.     

Crystal and molecular structure of N-(1-silatranylmethyl)benzimidazole

The crystal and molecular structure of N-(1-silatranylmethyl)benzimidazole was established by X-ray diffraction. The coordination polyhedron of the silicon atom in this molecule is a trigonal bipyramid. The bond lengths and angles of the N-(1-silatranylmethyl)benzimidazole (SMBI) molecule are compared with the corresponding values for other derivatives of this heterocycle. The silatranylmethyl group, having a high electron-donor inductive effect, does not increase the total aromaticity of the SMBI molecule.     

Nonrigid molecule effects in molecules with linear or nongeometrically equivalent equilibrium configurations

A theoretical study is made of the states of nonrigid molecules, extending earlier work to apply Longuet–Higgins' symmetry group of feasible permutation/inversions in two previously untreated cases. The first involves nonrigid molecule processes between different stereoisomers, that is between molecular equilibrium configurations of different geometrical shapes. The second takes into account nonrigid molecule processes in linear molecules. The theory is applied to the specific case of nonrigid molecule effects in the butyl ion C₄H (case i), and the form of the nonrigid molecule energy levels and spectra are determined. The theory is also applied to determine the nonrigid molecule energy levels in linear H₂F₂ (case ii).     

Surface-enhanced Raman scattering of 1-butanethiol in silver sol

The surface-enhanced Raman scattering (SERS) of 1-butanethiol was investigated in a silver sol. The molecule was found to be chemisorbed dissociatively on the silver surface by rupture of its SH bond. It is concluded that conformers of 1-butanethiol adsorbed selectively on the silver surface, the trans conformer around the C (1)C (2) axes being more likely adsorbed when the bulk concentration of the molecule is enough for the full monolayer coverage. The vibrational assignment of the molecule in liquid phase has also been refined by using the SERS data.     

Raman spectroscopic study of 2-methyl-1-propanethiol in silver sol

The surface-enhanced Raman scattering (SERS) of 2-methyl-1-propanethiol is investigated in a silver sol. As for other thiols, the molecule appears to be chemisorbed dissociatively on the silver surface by rupture of its S---H bond. At the bulk concentration sufficient for full monolayer coverage, the P_C conformer with a methyl group rans to the sulfur atom is found to be the most advantageous form on the surface. The vibrational assignments for the 2-methyl-1-propanethiol molecule are made by using the SERS data in conjunction with the previously reported normal-mode assignments for the corresponding alkyl chloride molecule, 1-chloro-2-methylpropane.     

Structural aspects of water in 1-octanol

Water-saturated 1-octanol, extensively used for studies of the distribution of organic solutes, is subjected to structural analysis in terms of the neighbors each molecule has. This is based on thermodynamic information on the system from the literature. The local composition of a given water molecule is richer in water than the bulk composition, and, conversely, for the local composition near a 1-octanol molecule. At saturation (mole fraction of water of 0.275 in the organic phase) the excess (deficiency) of the mole fraction of water is 0.197 (–0.075) near water (1-octanol) molecules.     

O3分子在CuO(110)面吸附的密度泛函理论研究

应用密度泛函理论研究了O3分子在2×1 CuO(110)面(S1)和掺杂一个Fe原子的2×1 CuO(110)面(S2)的吸附过程和电子特性. 计算结果表明, O3分子与表面S1和S2有很强的相互作用, O3分子在表面吸附反应的活化能和反应能均为负值, 反应很容易进行. 态密度和电荷密度分析结果进一步证实了O3分子在S1上吸附是桥位化学吸附, 形成表面臭氧化物, 在S2上吸附分解为1个被吸附的表面氧原子和1个自由氧分子. 电子特性分析表明, O3分子与S1和S2相互作用的本质是O3分子的价轨道2p与CuO(110)表面杂化轨道的相互作用.     

Environmental‐Confinement‐Induced Stability Enhancement of Chiral Molecules

We computationally study the transition process of a chiral difluorobenzo[c]phenanthrene (DFBcPh) molecule within non‐polar fullerene C₂₆₀ to explore the confinement effect. We find blue‐shifts in the infrared and Raman spectra of the molecule inside the fullerene relative to those of isolated systems. Six types of spectrum features of the molecule appear in the 0–60 cm^?1 band. Interestingly, the energy barrier of the chiral transformation of the molecule is elevated by 15.88 kcal mol^?1 upon the confinement by the fullerene, indicating improvement in the stability of the enantiomers. The protection by C₂₆₀ lowers the highest occupied molecular orbital energy level and lifts the lowest unoccupied molecular orbital energy level of the chiral molecule such that the chiral molecule is further chemically stabilized. We concluded that the confinement environment has an impact at the nanoscale on the enantiomer transformation process of the chiral molecule.     

β-Cyclodextrin Inclusion Complexes of 2-Hydroxyfluorene and 2-Hydroxy-9-fluorenone: Differences in Stoichiometry and Excited State Prototropic Equilibrium

We report that 1:1 and 1:2 complexes are formed for 2-hydroxy-9-fluorenone with β-cyclodextrin (β-CD) and that there is an unusual red shift in emission at higher concentrations of β-CD. Between different stoichiometries of the complexes the titrimetric curves for the neutral–anionic equilibria for the guests differ drastically and so do the excited state pK values. The formation of an 1:1 inclusion complex with 2-hydroxy-9-fluorenone (2HFN) as the guest in β-CD with the binding constant (K) of 606.65 L·mol^?1 was determined. The ground and excited state pK _a values for the neutral–mono-anion equilibrium are not affected by β-CD. Hence the hydroxyl group is considered exposed in the aqueous environment. Two different types of inclusion complexes of 2HFN were observed in β-CD. The 1:2 complex of 2HFN shows a red shift from the 1:1 complex and is less fluorescent that the 1:1 complex. The red shift reveals that the 1:2 complex is more stabilized than the 1:1 complex. The excited state pK _a values in both complexes with β-CD are higher that those in aqueous solution. This shows that the complexation makes the molecule less acidic in the S1 state. The β-CD molecule is perceived as not able to encapsulate the 2HFN molecule fully, but the larger rim of the β-CD comes closer to the C=O group. The other half of the 2HFN molecule is encapsulated by the second β-CD molecule and thus there is formation of the 1:2 inclusion complex at higher concentrations of β-CD.     

Elucidating the mechanism of binding of chromate to cucurbit[6]uril: a DFT study

We report the binding of chromate, a toxic heavy metal ion to the macrocyclic host molecule, cucurbituril using density functional theory. Due to the anionic nature of the guest molecule and the portals of the host molecule, we propose that the binding mechanism should be assisted by cations. The calculated barrier for chromate binding to cucurbituril is found to be?~17?kcal?mol^?1. The large barrier can be attributed to portal opening of the host molecule, electrostatic repulsion between the guest molecule and the portals of the host molecule and the solvent re-organization around guest molecule.     

A reversible minimum-to-minimum mapping method for the calculation of free-energy differences

A general method is introduced for the calculation of the free-energy difference between two systems, 0 and 1, with configuration spaces omega(0), omega(1) of the same dimensionality. The method relies upon establishing a objective mapping between disjoint subsets gamma(i)(0) of omega(0) and corresponding disjoint subsets gamma(i)(1) of omega(1), and averaging a function of the ratio of configurational integrals over gamma(i)(0) and gamma(i)(1) with respect to the probability densities of the two systems. The mapped subsets gamma(i)(0) and gamma(i)(1) need not span the entire configuration spaces omega(0) and omega(1). The method is applied for the calculation of the excess chemical potential mu(ex) in a Lennard-Jones (LJ) fluid. In this case, omega(0) is the configuration space of a (N-1) real molecule plus one ideal-gas molecule system, while omega(1) is the configuration space of a N real molecule system occupying the same volume. Gamma(i)(0) and gamma(i)(1) are constructed from hyperspheres of the same radius centered at minimum-energy configurations of a set of "active" molecules lying within distance a from the ideal-gas molecule and the last real molecule, respectively. An algorithm is described for sampling gamma(i)(0) and gamma(i)(1) given a point in omega(0) or in omega(1). The algorithm encompasses three steps: "quenching" (minimization with respect to the active-molecule degrees of freedom), "mutation" (gradual conversion of the ideal-gas molecule into a real molecule, with simultaneous minimization of the energy with respect to the active-molecule degrees of freedom), and "excitation" (generation of points on a hypersphere centered at the active-molecule energy minimum). These steps are also carried out in reverse, as required by the bijective nature of the mapping. The mutation step, which establishes a reversible mapping between energy minima with respect to the active degrees of freedom of systems 0 and 1, ensures that excluded volume interactions emerging in the process of converting the ideal-gas molecule into a real molecule are relieved through appropriate rearrangement of the surrounding active molecules. Thus, the insertion problem plaguing traditional methods for the calculation of chemical potential at high densities is alleviated. Results are presented at two state points of the LJ system for a variety of radii a of the active domain. It is shown that the estimated values of mu(ex) are correct in all cases and subject to an order of magnitude lower statistical uncertainty than values based on the same number of Widom [J. Chem. Phys. 39, 2808 (1963)] insertions at high fluid densities. Optimal settings for the new algorithm are identified and distributions of the quantities involved in it [number of active molecules, energy at the sampled minima of systems 0 and 1, and free-energy differences between subsets gamma(i)(0) and gamma(i)(1) that are mapped onto each other] are explored.     

Crystal and molecular structure of 1-(trimethylsilylmethyl)benzotriazole

The crystal and molecular structure of 1-(trimethylsilylmethyl)benzotriazole has been established by X-ray diffraction (XRD) analysis. The coordination polyhedron of the silicon atom in this molecule is a tetrahedron. The bond lengths and angles of the 1-(trimethylsilylmethyl)benzotriazole molecule were compared with those of related crystal structures.     

CS与NO分子反应势能面的理论研究

应用量子化学从头计算和密度泛函理论(DFT)对CS分子和NO分子的反应机理进行了研究. 在B3LYP/6- 311G**和CCSD(T)/6-311G**水平上计算了CS分子与NO分子反应的二重态和四重态反应势能面. 计算结果表明, 二重态反应势能面中, CS分子的C端和NO的N端连接是主要的反应方式. 反应物先经过过渡态TS1, 形成具有直线结构的中间体1 (CSNO). 中间体1经过一系列异构化得到主要产物P₁ (CO＋SN). 此反应是放热反应, 反应热为－183.75 kJ/mol . 而四重态由于反应入口势垒过高, 是不重要的.     

Fluorescent gel from a self-assembling new chromophoric moiety containing azobenzene based tetraamide

A new chromophoric low molecular weight (LMW) organic molecule, 1, was synthesized, and it forms gels in various organic solvents including toluene, o-xylene, m-xylene and p-xylene. The resultant gel phase materials exhibit enhanced and red-shifted fluorescence emission in the respective gelling solvents. This gelator molecule is self-assembled using various noncovalent interactions including hydrogen bonding, pi-pi staking and van der Waals interactions to get the gel phase materials. The molecule 1 is very weakly fluorescent in solution, but its intensity is increased by almost 40 times in their respective gelled state depending on the nature of the gelling solvents. Self-assembly of this molecule in the above-mentioned organic solvents gives an elongated nanofibrillar network that can be visualized through Field Emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and atomic force microscopy (AFM).