Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

Probing structure in the polymorphic domain of the L-enantiomer of N-benzoyl-phenylalanine by means of 2D solid-state NMR spectroscopy and DFT calculations

A study of polymorphism using a range of solid-state NMR techniques is presented. We demonstrate the existence of at least six polymorphs in a sample of N-benzoyl-L-phenylalanine. We also present methodology for the characterization of the protonation state, hydrogen bonding, and molecular conformation for the polymorphs, together with results of such a characterization for one of the polymorphs present in our sample. DFT modeling is used to investigate the separate effects hydrogen bonding and molecular conformation have on the chemical shift tensor.     

The Structure of Tris(3',5'-dimethylpyrazol-1-yl)-s-triazine and Its Use as a Ligand in Coordination Chemistry

The crystal and molecular structure of the title compound (Me₂-TPzT) has been determined by X-ray analysis. The observed molecular conformation presents the nitrogen atoms of three pyrazole rings in the same relative positions. The molecules are joined through intermolecular contacts forming chains that are arranged in a distorted hexagonal symmetry. Two complexes containing this ligand have been prepared: [{Pd(en)}₃(Me₂-TPzT)](PF₆)₆ and [{Ag(PPh₃)}3(Me₂-TPzT)](ClO₄)₃, which, due to their insolubility, have been characterized only by microanalysis, IR, ¹H NMR and, in the latter case, by mass spectrometry.     

Molecular-dynamics simulation for the characterization of liquid chromatographic stationary phase: effect of temperature.

The influence of temperature on the surface structure of the octadecylsilica (ODS) bonded phase was investigated with a molecular dynamics (MD) simulation. The MD simulation was applied to a molecular model consisting of three parts: amorphous silica base, dimethyloctadecylsilyl ligands and n-hexane as a mobile phase solvent. More detailed information on the effect of temperature was obtained at the low temperature region than that reported in our previous study. The motion of ODS ligands could be estimated by the mean square displacement (MSD) of the terminal carbon atoms of ODS ligands. The gauche fraction in the ODS ligand conformation can also be estimated to obtain the ligand conformation for each simulation condition in detail. It can be seen that an elevated temperature induced the more bent ligand conformation. The trend has a good agreement to that of the results experimentally observed by using various spectroscopic techniques such as nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FT-IR), and Raman spectroscopy.     

一种基于2, 2'-二吡啶胺功能化的新型空间位阻型9, 9'-二芳基芴的设计、合成及其光电性质研究

用2-溴吡啶通过乌尔曼反应修饰9-(4-苯胺基)-9-苯基芴合成了一种具有大体积空间位阻的双极性分子(PFPhDPy),这种化合物因其大的空间位阻、芴优异的双极型传输特性、共轭阻断结构以及吸电子的吡啶官能团而有望获得良好的热稳定性、稳定的无定形态、高的三线态能级和良好的双极性特征.热重分析曲线表明其失重5%的分解温度为336℃.差示扫描量热曲线显示将该化合物加热到190℃既没有熔化现象也没有结晶现象,意味着该化合物具有高的形貌稳定性.通过密度泛函理论计算,该化合物的最高占有轨道(HOMO)和最低未占有轨道(LUMO)完全分离,说明该化合物具有双极性特征,通过磷光光谱得到三线态能级为3.0 eV.紫外光谱显示该化合物不依赖于溶剂效应的三个特征吸收峰分别为276、298和308 nm.荧光光谱在二氯甲烷、乙酸乙酯、乙醇和乙腈溶剂中随着溶剂的极性增加光谱发生蓝移,其最大发射峰从390 nm转变为363 nm.另外,该化合物的结构分别通过基质辅助激光解析电离飞行时间质谱(MALDI-TOF MS)、氢核磁共振(¹H NMR)和碳核磁共振(¹³C NMR)谱进行了结构表征.     

Effect of molecular weight on the polymorphic transformation of isotactic poly(1-butene)

The effect of molecular weight on the polymorphic transformation of isotactic poly(1-butene)(iPB) under room temperature had been investigated by fourier transform infrared spectroscopy(FT-IR). The phase transformation time, phase transformation rate and phase transformation time difference between phase I and phase II at a given transformation degree were used to analysis the phase transformation kinetics of iPB aging at room temperature. The results show that the reduction of phase II can occur quickly at room temperature and seem less dependent on the molecular weight. However, the molecular weight has great effect on the formation of phase I. When the phase transformation degree for phase I reach 90%, a distinct transformation time difference can be observed. In order to clearly explain the difference in the reduction of phase II and the growth of phase I, a phase transformation model from the chain conformation level for iPB with different molecular weight have been drawn. DSC analysis was used to support the proposed model.     

Synthesis of 2′-Deoxy-5-(isothiazol-5-yl)uridine and Its Interaction with the HSV-1 Thymidine Kinase

2′-Deoxy-5-(isothiazol-5-yl)uridine ( 12 ) was synthesized starting from 2′-deoxy-5-iodouridine using a Pd-catalysed cross-coupling reaction with propiolaldehyde diethyl acetal followed by deprotection and ring closure using thiosulfate. 2′-Deoxyuridine 12 has a particular place among the 5-heteroaryl-substituted 2′-deoxyuridines in that it has a high affinity for herpes simplex virus type 1 (HSV-1)-encoded thymidine kinase (TK) without antiviral activity. Biochemical studies revealed that 12 is a substrate for viral TK. We further investigated the interaction of 12 with the HSV-1 thymidine kinase. The conformation of 12 in solution was established by NMR spectroscopy. The most stable conformer 12A has the S-atom of the isothiazole ring placed in the neighbourhood of the C(4)?O group of the pyrimidine moiety. The compound was docked in its most stable conformation in the active site of HSV-1 TK and subjected to energy minimization. This demonstrated that the isothiazole moiety binds in a cavity lined by the side chains of Tyr-132, Arg-163, Ala-167, and Ala-168 and that the C(3) atom of the isothiazole moiety is located in close proximity of the phenolic O-atom of Tyr-132 and the aliphatic part of the Arg-163 side chain.     

Simvastatin: structure solution of two new low-temperature phases from synchrotron powder diffraction and ss-NMR

Simvastatin is a substance used for the treatment of hypercholesterolemia. In addition to the already known room temperature structure of simvastatin (Čejka et al. in Acta Cryst C59:o428, 2003) two new low-temperature polymorphs were found by X-ray powder diffraction with the phase transition at 261 and 223 K (later confirmed by DSC to be 272 and 232 K). The main differences among three polymorphs consist in the side-chains conformation only and the phase changes are fully reversible. The structures of the polymorphs were studied by the powder diffraction based on synchrotron radiation as well as by solid-state NMR spectroscopy.     

(6,17-Dimethyl-8,15-diphenyldibenzo[b,i][1,4,8,11]-tetra-aza[14]annulenato)nickel(II) in solids: two guest-free polymorphs and inclusion compounds with methylene chloride and fullerene (C(60))-carbon disulfide

Two guest-free polymorphs and two inclusion compounds of the macrocyclic title complex [NiL] have been isolated and characterized with single-crystal and/or powder XRD, solid-state (13)C NMR, and other methods. The inclusion compound with methylene chloride, [NiL](CH(2)Cl(2)), is stable in air and thermally stable up to approximately 128 degrees C. Its crystal structure is consistent with van der Waals packing of the host [NiL] and guest CH(2)Cl(2) molecules. The host complex has square-planar coordination of the nickel(II) center with four nitrogen atoms of the macrocycle with an average Ni-N distance of 1.86 A. The molecule has a saddle-shaped conformation with the guest molecule located between one phenylene and two phenyl rings of the host molecule. Isostructural compounds with chloroform and 2-chloropropane form only as mixtures along with a guest-free host polymorph. The inclusion compound with C(60) has a composition 3[NiL]*(C(60))*2(CS(2)) and here also the crystal structure is consistent with a van der Waals type of packing. Three crystallographically inequivalent [NiL] molecules have geometries similar to that in the inclusion compound with methylene chloride. The concave surfaces of the complex molecules form a spherical cavity for the C(60) molecule. At -100 degrees C the C(60) molecule is disordered over two orientations centered at the same site. (13)C NMR studies at room temperature show that the C(60) molecule is undergoing rapid pseudo-isotropic rotation. The stability and other properties of the title and related complexes are discussed.     

N‐Methyl‐N‐phenylaminomethyl 2‐naphthyl ketone: an X‐ray diffraction and density functional theory study

The crystallographically observed molecular structure of the title compound, C₁₉H₁₇NO, and its inverted counterpart are compared with that calculated by density functional theory (DFT) at the B3LYP/6‐311++G(d,p) level. The results from both methods suggest that the observed molecular conformation of the title compound is primarily determined by intermolecular interactions in the crystal structure. The periodic organization of the molecules is stabilized by weak C—H...O and C—H...π hydrogen bonds and thus a two‐dimensional puckered network consisting of R₄⁴(22) and R₄⁴(38) ring motifs is established. The title molecule has a (+)‐antiperiplanar conformation about the C—C bond in the aminoacetone bridge. The pyramidal geometry observed around the vertex N atom is flattened by the presence of bulky phenyl and naphthylethanone fragments.     

3-(2-对甲苯基乙烯基)-5(4H)-异噁唑酮的合成、晶体结构、1H NMR及其异构化研究

采用甲硫酯与NH2OH·HCl在室温条件下反应,合成了3-(2-对甲苯基乙烯基)-5(4H)-异唑酮,通过单晶X射线衍射确定了产物的结构.由1HNMR确定的构型与晶体结构完全一致,表明标题化合物在弱极性溶剂(如乙醚和氯仿)中是稳定的.半经验AM1和PM3计算的C7和C8净电荷(分别为-0.077,-0.101)可能是H7和H8化学位移(分别为6.83和6.96)很接近的主要原因.B3LYP/6-311G**基组计算的异构体能量数据表明,3-(2-对甲苯基乙烯基)-5(4H)-异唑酮是最稳定的构型     

Molecular mechanism for the cross-nucleation between polymorphs

We use molecular simulations to study the early stages of crystallization in a supercooled liquid of Lennard-Jones particles. We observe the onset of concomitant polymorphism and demonstrate that this phenomenon results from the cross-nucleation of a metastable polymorph on the stable polymorph. We also show that cross-nucleation is selective as it only takes place between polymorphs of almost equivalent free energy. Our simulations provide detailed insights into the molecular mechanism underlying concomitant polymorphism and cross-nucleation between polymorphs.     

2-取代酰氨基-5-去氢枞基-1,3,4-噻二唑衍生物的合成及杀菌活性

为了寻找具有更高生物活性的新颖先导化合物,本文以去氢枞酸为原料,设计并合成了11个具有1,3,4-噻二唑骨架的新型去氢枞酸衍生物,通过1H NMR、13C NMR、IR、EI-MS和元素分析确认了目标产物的结构。初步的生物活性测试结果表明,大部分化合物具有一定的杀菌活性,其中,化合物2在浓度为50mg/L时对番茄早疫病菌的抑制率达88.9%。     

Synthesis and properties of stable 2-metallanaphthalenes of heavier group 14 elements

The first stable neutral stannaaromatic compound, 2-stannanaphthalene , was synthesized by taking advantage of an extremely bulky and efficient steric protection group, 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl (Tbt). The molecular structure and aromaticity of were discussed on the basis of X-ray crystallographic analysis, NMR, UV-vis, and Raman spectroscopy, cyclic voltammetry, and theoretical calculations. 2-Germanaphthalene , which has a framework similar to that of , was synthesized for comparison, and systematic elucidation was made for the properties of 2-metallanaphthalene systems containing a heavier group 14 element (Si, Ge, or Sn).     

异丙氧基-异羟肟酸-氧钒（V）配合物的合成、晶体结构和量子化学研究

以苯甲酰异羟肟酸为配体，首先合成四价氧钒化合物，以此为基础合成了标题 化合物，并用元素分析，红外光谱，~1H NMR，~(13)C NMR，~(15)V NMR，电子吸 收光谱等，分别对它进行了表征，其结构用单晶X射线衍射法测定，晶体属三斜晶 系，P1-bar空间群，所得晶体学参数为a = 1.1119(3) nm，b = 1.1735(3) nm，c = 0.8660(2) nm，α = 96.84(1)°，β = 106.93)(1)°，γ = 88.97(1)°，V = 1.0731(2) nm~3，D_c = 1.415 g/cm~3，Z = 2，F(000) = 478，μ = 5.06 cm~(-1)。采取ab initio(GTO-6-31d)方法对标题化合物的结构单元的成键情况进 行了分析，讨论了化合物的稳定性、分子轨道能量、原子静电荷分布等情况。     

(3R,4S)-4-(4-Fluorophenyl)-3-hydroxymethyl-1-methylpiperidine: conformation and structure monitoring by vibrational circular dichroism.

Absorption and vibrational circular dichroism (VCD) spectra of the title compound, a common intermediate in synthesis of many pharmaceuticals, were measured and analyzed in order to determine its absolute configuration and prevailing conformations. The analysis was combined with a systematic conformer search based on relative energies as well as with comparison of experimental and computed NMR shifts. The spectra were interpreted on the basis of ab initio simulations. The results indicate that the compound adopts exclusively a chair conformation of the piperidine ring with all the fluorophenyl, hydroxymethyl, and methyl substituents attached in equatorial positions. A limited rotation of the hydroxymethyl group is most consistent with the observed VCD pattern. VCD parameters were found significantly more sensitive to conformational changes than absorption or NMR. Concentration dependence of the absorption spectra indicated aggregation in concentrated solutions, but involved hydrogen bonds probably do not influence molecular conformation.     

Three conformational polymorphs of di-mu-chlorotetrakis(1-methylboratabenzene)diyttrium: synthesis, x-ray structures, quantum chemical calculations, and lattice energy minimizations

The reaction of yttrium trichloride with lithium 1-methylboratabenzene (1/2) in toluene (110 degrees C, 3 days) afforded the donor-free dinuclear sandwich complex [(C(5)H(5)BMe)(2)Y(mu-Cl)](2) (1) in 85% yield as pale-yellow crystals. By means of single crystal and powder diffraction methods, three conformational polymorphs, alpha-1 [P2(1)/n (No. 14), monoclinic, a = 6.6124(8) A, b = 14.352(9) A, c = 14.120(1) A, beta = 95.57(1) degrees, V = 1333.7(9) A(3), Z = 2], beta-1 [P2(1)/a (No. 14), monoclinic, a = 8.542(2) A, b = 13.712(6) A, c = 11.76(1) A, beta = 102.60(4) degrees, V = 1344.5(13) A(3), Z = 2], and gamma-1 [Pbca (No. 61), orthorhombic, a = 20.091(5) A, b = 13.527(3) A, c = 9.976(2) A, V = 2711.2(11) A(3), Z = 4], were characterized in the solid state of 1. The molecules in the three phases vary remarkably in the rotational position of boratabenzene ligands with differences of 91.1, 133.1, and 24.9 degrees between each pair. DFT calculations at the B3LYP/LanL2DZ level reveal that the three molecular structures observed in the solid state correspond closely to three minima on the gas-phase potential energy surface. The beta conformation is 2.8 and 7.2 kJ/mol more stable than the alpha and gamma conformations, respectively. Lattice energy minimizations predict that the alpha-1 phase is about 5.5 and 18.7 kJ mol(-)(1) more stable than the beta-1 and gamma-1 modifications, in agreement with the packing coefficients and the molecular volumes of the three crystal structures. While the alpha-1 and beta-1 modifications have comparable total energies, the gamma-1 form is less stable. The total energy differences among the polymorphs are greater than generally expected.     

The synthesis and characterization of α- and β-1, 1-diiodo-3,4-benzo-1-telluracyclopentane,C8H8Tel2

Elemental Tellurium reacts with α,α′-dichloro-o-xylene and NaI in 2-methoxyethanol to form 1,1-diiodo-3,4-benzo-1-telluracyclopentane in 83% yield. C₈H₈TeI₂ is molecular in acetone, methylene chloride and methyl ethyl ketone, but ionic in DMF. Two crystalline modifications of the compound have been isolated from 2-methoxyethanol. The yellow-orange or α form is monoclini?, space group P2₁/c; the orange-red or β form is also monoclinic, space group I2/c. Infrared, optical and mass spectral data, along with solution UV, NMR, molecular weight and conductivity data, suggest that the two crystalline modifications are plymorphs, possibly differing in the degree and type of heavy atom interaction. In 2-methoxyethanol the β form undergoes a solution phase transformation to the stable α form. Both forms are thermochromic.     

A polycatenar mesogen with a perfluorinated moiety showing continuous phase transformation between a smectic A phase and a structured,fluid, optically isotropic phase

A polycatenar mesogen consisting of a four aromatic ring system with three long alkoxy chains and a bulky perfluorinated substituent has been synthesized and found to show the polymorphism of a cubic phase, a columnar phase and a smectic A phase, including a structured, fluid, optically isotropic phase with the phase transformation between the smectic A phase and the isotropic phase occurring continuously.     

Two polymorphs of N1,N4‐bis(5‐hydroxypenta‐1,3‐diynyl)‐N1,N4‐diphenylbenzene‐1,4‐diamine

The title compound, C₂₈H₂₀N₂O₂, forms two conformational polymorphs, (I) and (II), where the molecular structures are similar except for the orientation of the two hydroxy groups. In (I), which was obtained by slow evaporation from chloroform, the two hydroxy groups have an anti conformation. The molecules form a sheet structure within the ac plane, where the hydroxy groups form zigzag hydrogen bonds. In (II), which was obtained by slow evaporation from acetonitrile, the two hydroxy groups have a syn conformation. The molecules form a double‐sheet structure within the ab plane, where the hydroxy groups form 4‐helix hydrogen bonds.