Application of molecular mechanics to refine and understand the crystal structure of polythiophene and its oligomers

A molecular mechanics computational procedure, previously used for the refinement and the analysis of several crystalline polymers, was applied to investigate the crystal structures of the tetramer (T4) and hexamer (T6) of thiophene, as well as the crystal structure of polythiophene (PT). Simultaneous minimization of intra- and intermolecular energies of the T4 and T6 structures, obtained by Rietveld analysis of powder X-ray diffraction profiles, leads to molecular conformations showing smaller deviations from the ring co-planarity than the original models. For both oligomers the calculations confirm that the molecular centre of inversion is not a crystallographic centre of symmetry, as also revealed by X-ray diffraction of the T6 single crystal. This surprising effect appears to arise from intermolecular interactions between the terminal residues, hence is not relevant with respect to the PT polymer structure. The small energy cost for constraining the molecules at the crystallographic centre of symmetry is in agreement with experimental findings that reveal the existence of polymorphs for both T4 and T6. The calculations on the T6 single crystal were used to upgrade the MM2-like force field, which was then used to determine the minimum-energy model of the monoclinic crystal structure of polythiophene.     

N,N′-双(1H-苯骈三氮唑基-1-甲基)-硫脲的合成和晶体结构

参照文献报道的合成方法,以苯骈三氮唑和硫脲为原料,以冰醋酸为溶剂,制备了双苯骈三氮唑取代的化合物N,N′-双(1H-苯骈三氮唑基-1-甲基)-硫脲;经进一步培养得到其单晶;利用元素分析和红外光谱初步分析了产物的组成和结构,利用X射线单晶衍射分析了其分子结构.     

含能配位聚合物[Cu(tza)2]n的晶体结构、热分析、感度和催化性能

以碱式碳酸铜和四氮唑乙酸在水中反应制备得到四唑乙酸铜(II)含能配位聚合物, 并培养出单晶. 运用元素分析, FT-IR分析和X-射线单晶衍射对标题配合物的组成和结构进行了全面的表征. 采用差示扫描量热分析(DSC)和热重-微分热重分析(TG-DTG)研究了标题配合物的热分解过程, 表明标题配合物的热分解主要包含三个放热峰. 用Kissinger和Ozawa-Doyle法对标题配合物的第一放热分解过程进行了动力学研究, 计算得到其活化能为356.1 kJ/mol. 对配合物的撞击、摩擦、火焰感度和5s爆发点测试表明该配合物具有一定的感度, 有望作为含能材料应用于相关领域. 同时研究了标题配合物对RDX热分解的影响, 结果表明: 标题配合物可以使RDX的放热分解峰的温度提前16.4 ℃,分解速度加快, 对RDX具有良好的催化作用.     

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data.     

Synthesis of 1-(2-Fluorophenyl)pyrazoles by 1,3-Dipolar Cycloaddition of the Corresponding Sydnones

3-Arylsydnones bearing fluorine and bromine atoms on the benzene ring were synthesized from N-nitroso-2-fluorophenylglycines and characterized by NMR spectroscopy. These were employed further in synthesis of the corresponding 1-(2-fluorophenyl)pyrazoles by 1,3-dipolar cycloaddition reaction with dimethyl acetylenedicarboxylate (DMAD) as activated dipolarophile. The sydnones as reaction intermediates were characterized by single crystal X-ray diffraction analysis showing interesting features such as halogen bonding as an important interaction in modeling the crystal structure.     

From crystal to crystal: A reconstructive solid-state reaction

The crystal structure of the Lewis acid-base adduct of 2-chloro-2-boraindane and diethylether was determined by X-ray diffraction. After abstraction of the boron-coordinated Et₂O molecule in vacuo, the crystal and molecular structure of the solvent-free boraindane, earlier synthesized by Kaufmann and Schacht [1], was studied on the resulting crystalline material. The different crystal packing in both structures and a diffraction experiment on an oriented single crystal showed that the reaction is reconstructive and that a rearrangement of the molecules parallels the change in molecular geometry.     

How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data

Many crystalline solids cannot be prepared as single crystals of sufficient size and/or quality for structure determination to be carried out using single crystal X-ray diffraction techniques. In such cases, when only polycrystalline powders of a material are available, it is necessary instead to tackle structure determination using powder X-ray diffraction. This article highlights recent developments in the opportunities for determining crystal structures directly from powder diffraction data, focusing on the case of molecular solids and giving particular attention to the most challenging stage of the structure determination process, namely the structure solution stage. In particular, the direct-space strategy for structure solution is highlighted, as this approach has opened up new opportunities for the structure determination of molecular solids. The article gives an overview of the current state-of-the-art in structure determination of molecular solids from powder diffraction data. Relevant fundamental aspects of the techniques in this field are described, and examples are given to highlight the application of these techniques to determine crystal structures of molecular materials.     

Theoretical and experimental studies of the structure and intermolecular interactions in 2-biphenylmethanole

The crystalline structure of 2-biphenylmethanol has been investigated by the radiographic method at room temperature, and its IR transmission spectra were measured in the 400–4000 cm^?1 range. Structural-dynamic models of free molecules of 2-biphenylmethanol, biphenyl and methanol, hydrogen-bonded complexes of 2-biphenylmethanol with methanol and a tetramer of methanol molecules have been built by the density functional method (B3LYP/6-31G*). The structure, the energy, mechanical and electro-optical parameters, the frequency and intensity of normal vibrations in IR spectra of each of the mentioned molecular systems were calculated. The crystalline structure of 2-biphenylmethanol, its features determined by the hydrogen bond formation in the crystal has been found, its structure-forming role and energy were assessed, and IR spectra interpreted on the basis of single crystal X-ray diffraction data, the analysis of measured IR spectra, and results of molecular modeling.     

Crystal structure and DFT calculations of methanol {E-N′-(2-hydroxybenzlidene)benzohydrazido}dioxidomolybdenum (VI) complex

The crystal and molecular structure of methanol {E-N′-(2-hydroxybenzlidene)benzohydrazido}dioxidomolybdenum (VI) was determined by single crystal X-ray diffraction. B3LYP/DZP basis set theoretical calculations nicely reproduce the X-ray experimental geometry. The obtained results are discussed in connection with the electronic and structural properties of the compound.     

An unusual conformation of 1,1′-dimethyl-isoindigo in crystals

The crystal and molecular structure of 1,1′-dimethyl-isoindigo is studied by single crystal X-ray diffraction analysis. It is shown that the molecules of 1,1′-dimethyl-isoindigo are nonplanar due to the rotation of two oxindole rings relative to the double bond.     

Crystal and molecular structure of tigogenin

Tigogenin [(25R)-5α-spirostan-3β-o1] was isolated from Digitalis lanata Ehrh., and its crystal and molecular structure was determined by single crystal X-ray diffraction.     

An X-ray and DFT Computational Study on 1-（Naphthalene-2-yl）-2-（1H-pyrazol-1-yl） ethanone O-butyl Oxime

The title compound, 1-(naphthalene-2-yl)-2-(1H-pyrazol-1-yl)ethanone O-butyl oxime, I, was synthesized. The crystal and molecular structures of I were determined by IR, 1H-NMR, mass spectrum, elemental analysis and X-ray single crystal diffraction. Molecular geometry from X-ray experiment of I in the ground state was compared using the Density Functional Theory (DFT) with B3LYP/6-311G(d,p) basis set. In addition, DFT calculation, molecular electrostatic potentials (MEP) and frontier molecular orbitals of I were performed at the B3LYP/6-311G(d,p) level of the theory.     

Synthesis, structural characterization and conformational aspects of nostoclide analogues

The synthesis and structural analysis of a set of nostoclide analogues with potential herbicide activity is described. The influence of intra- and intermolecular hydrogen bonding, as well as other interactions on the conformation and packing of the compounds is thoroughly described using DFT calculations and single crystal X-ray diffraction analyses. All lactones exhibited the Z configuration as confirmed by NOESY experiments and by single crystal X-ray diffraction measurements.     

X-ray diffraction and quantum-chemical analysis of a single crystal of 2,5-dimethyl-3,4-dihydro-2h-pyran-2-carboxylic acid

The structure of synthesized 2,5-dimethyl-3,4-dihydro-2H-pyran-2-carboxylic acid was investigated by the single crystal X-ray diffraction analysis method. It was established that the molecule of the acid exists in the form of the endo isomer while the single crystal exists as a racemate of the two enantiomeric endo stereomers. Quantum-chemical calculations of a model of the macrocell of the acid by means of the semiempirical MOPAC2009 program agree well with the X-ray diffraction data.     

Physico-chemical characterization of an active pharmaceutical ingredient

The physico-chemical properties and polymorphism of a new active pharmaceutical ingredient entity has been analyzed and the gain of knowledge during the chemical development of the substance is described. Initial crystallization revealed an anhydrous crystal form with good crystallinity and a single, sharp DSC melting peak at 171°C and a straightforward development of this crystal form seemed possible. However, during polymorphism screening, new crystalline forms were detected that were often analyzed as mixtures of crystal forms. The process of characterization and identification of the different crystalline forms and its thermodynamical relationship has been supported by a combination of experimental and computational work including determination of the three-dimensional structures of the crystal forms. The crystal structure of one polymorphic form was solved by single crystal X-ray structure analysis. Unfortunately, Mod B resisted in formation of suitable single crystals, but its structure could be solved by high resolution powder diffraction data analysis using synchrotron radiation. Calculation of the theoretical X-ray powder diffraction pattern from three dimensional crystal coordinates allowed an unambiguous identification of the different crystalline forms. Two polymorphic crystal forms of the API-CG3, named Mod A and Mod B, are enantiotropic whereas Mod B is the most stable polymorph at room temperature up to about 50°C and Mod A at temperatures above 50°C. The mechanism of the solid-solid transition can be explained by analyzing the molecular packing information gained from the single crystal structures. A third crystalline form with the highest melting peak turned out to be not a polymorphic or pseudopolymorphic crystal modification of our API-CG3 but a chemically different substance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Single crystal X-ray diffraction study of 2,4,6-triazidopyridine and its 3,5-dibromosubstituted derivative

By the single crystal X-ray diffraction analysis in combination with quantum chemical calculations the molecular and crystal structures of high-energy 2,4,6-triazidopyridine and 2,4,6-triazido-3,5- dibromopyridine are studied; the dependence of structural parameters of their azido groups on the size of substituents in β-positions of the pyridine ring is analyzed. The effect of the intramolecular contact involving the central nitrogen atom of γ-azido groups in substituted triazides on their structure and properties is revealed.     

Growth and characterization of organic material 2-methylamino-5-chlorobenzophenone single crystal by modified vertical Bridgman technique

The organic material 2-methylamino-5-chlorobenzophenone single crystal has been grown by modified vertical Bridgman technique using the single wall ampoule with nano translation. The grown crystal was confirmed by single crystal and powder X-ray diffraction analyses. Fourier transform infrared analysis was used to identify the functional groups present in the grown crystal. High resolution X-ray diffraction studies show the crystalline perfection of the grown crystal. The optical property of the grown crystal was analyzed by UV-vis-NIR and photoluminescence spectral studies. The thermal behavior of the grown crystal was analyzed by thermogravimetric and differential thermal analyses. The dielectric measurements of the grown crystal were carried out with different frequencies and temperatures and the results indicate an increase in dielectric and conductivity parameters with the increase of temperature at all frequencies. The microhardness measurements were performed to analyze the mechanical property of the grown crystal.     

Growth and characterization of 2-hydroxy-4-methoxybenzophenone single crystal using modified vertical Bridgman technique

The 2-hydroxy-4-methoxybenzophenone single crystal has been grown by the modified vertical Bridgman technique using the double wall ampoule. The grown crystal was confirmed by single and powder X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy analyses. High resolution X-ray diffraction (HRXRD) analysis indicates the crystalline perfection of the grown crystal. The cutoff wavelength of the grown crystal was analyzed by optical studies. The dielectric measurements were carried out and the results indicate an increase in dielectric and conductivity parameters with the increase of temperature at all frequencies. The thermal property of the grown crystal was studied by thermo gravimetric (TG) and differential thermal analyses (DTA).     

室温固相反应一步合成N-亚水杨基-4-氨基安替比林

4-氨基安替比林与水杨酬醛通过室温固相反应合成N-亚水杨基-4-氨基安替比 林，反应无溶剂，15 min即可完成，产率达95%，用元素分析，IR，~1H NMR，X射 线粉末衍射和X射线单晶衍射对产物进行了表征。     

Impact of Crystal Habit on the Dissolution Rate and In Vivo Pharmacokinetics of Sorafenib Tosylate

The dissolution rate is the rate-limiting step for Biopharmaceutics Classification System (BCS) class II drugs to enhance their in vivo pharmacokinetic behaviors. There are some factors affecting the dissolution rate, such as polymorphism, particle size, and crystal habit. In this study, to improve the dissolution rate and enhance the in vivo pharmacokinetics of sorafenib tosylate (Sor-Tos), a BCS class II drug, two crystal habits of Sor-Tos were prepared. A plate-shaped crystal habit (ST-A) and a needle-shaped crystal habit (ST-B) were harvested by recrystallization from acetone (ACN) and n-butanol (BuOH), respectively. The surface chemistry of the two crystal habits was determined by powder X-ray diffraction (PXRD) data, molecular modeling, and face indexation analysis, and confirmed by X-ray photoelectron spectroscopy (XPS) data. The results showed that ST-B had a larger hydrophilic surface than ST-A, and subsequently a higher dissolution rate and a substantial enhancement of the in vivo pharmacokinetic performance of ST-B.