Crystal and molecular structure of methyl(±)-2-((1R,3R)-3-{ 2-[(3S)-1-ethyl-3-hydroxy-2-oxo-2,3-dihydro-1H-3-indolyl]acetyl}-2,2-dimethylcyclobutyl) acetate

The structure of methyl (±)-2-((1R,3R)-3-{ 2-[(3S)-1-ethyl-3-hydroxy-2-oxo-2,3-dihydro-1H-3-indolyl]acetyl}-2,2-dimethylcyclobutyl) acetate has been determined by single crystal X-ray diffraction. The crystal belongs to triclinic system; parameters of the unit cell are: a = 6.551(1) Å, b = 11.506(1) Å, c = 14.334(1) Å, α = 101.41(1)°, β = 97.57(1)°, γ = 104.72(1)°; space group P-1, Z = 2, composition C₂₁H₂₇NO₅. The structure of N-ethyloxindole fragment is usual for the present class of compounds. The configuration of the formed asymmetric carbon atom C(3) of the pyrrole ring along with the configuration of C(12) and C(14) atoms of 2,2-dimethylcyclobutane ring form the side chain of the molecule were determined. There is observed the generation of centrosymmetrical dimers in the crystal structure due to realized intermolecular hydrogen bond of O-H...O type, 2.808(2) Å.     

Characteristic features of intra- and intermolecular interactions in crystals of pyrrole-2-carbaldehyde isonicotinoylhydrazone and its hydrate

Pyrrole-2-carbaldehyde isonicotinoylhydrazone (1) and its hydrate [1·H₂O] (2) were studied by single-crystal X-ray diffraction analysis. The introduction of the pyrrole substituent into N"-substituted isonicotinic hydrazide (INH) causes the intramolecular redistribution of the electron density compared to those in INHs studied earlier, which increases the basicity of the hydrazone nitrogen atom (N") involved in intermolecular hydrogen bonding. This effect has not been observed in the structures of N"-substituted INHs and benzhydrazides studied previously. Intermolecular hydrogen bonds play a decisive role in the formation of the crystal structures of 1 and 2.     

黄芩苷的晶体结构研究

用乙醇-水溶液体系从黄芩中提取黄芩苷, 纯化得黄芩苷纯度为95.2%. 在步长0.0167°, 停留时间7.62 ms条件下对其粉末进行扫描, 获得较高质量粉末衍射谱图. 在运用密度泛函方法获得其分子低能量构象基础上, 采用直接空间搜索法解析其晶体结构, 得该样品属于单斜晶系, P21空间群, 晶胞参数为: a＝13.02 Å, b＝17.22 Å, c＝4.49 Å, α＝ γ＝90°, β＝95.40°, Z＝2, V＝1016.1 Å3. 结合自然键轨道理论分析, 表明结构中苷元部分杂环可能具有芳香性. 红外振动光谱结果发现, 共轭效应导致了羰基伸缩振动频率红移, 氢键的存在导致了羟基伸缩振动频率红移. 由分子间氢键的影响, 预测了其晶体生长特性.     

Hydrogen bond and the structures of 2-, 3-and 4-biphenylmethanols

Density functional theory (B3LYP/6-31G*) is applied to calculate structures, energy, dipole moment, polarizability, frequencies of normal vibrations in the harmonic approximation and intensities in vibrational spectra of 2-, 3-, and 4-biphenylmethanol molecules and their H-complexes that can form in crystalline, amorphous, and liquid phases. Based on the analysis of simulation results, the effect of the position of a methanol group in the molecule on its vibrational spectrum is discussed. The structure forming role of a hydrogen bonds in biphenylmethanols and the possibility of realization of two polymorphic modifications in 2-biphenylmethanol are stated. These modifications are: metastable monoclinic, in which each of four molecules of the unit cell is a link of a chain H-associate; and stable triclinic, in which four molecules of the unit cell organize an H-complex in the form of a cyclic tetramer. It is found that crystalline samples of 3-and 4-biphenylmethanols consist of chain H-associates. A glass-like sample of 2BPhM being a mixture of H-complexes consisting of cyclic tetramers and chain associates contains crystalline nuclei of triclinic and monoclinic polymorphous modifications in the supercooled state. In a liquid sample of 2BPhm, chain H-associates and free molecules are realized.     

Vibrational spectra of 2-biphenylmethanol. Spectrum simulation and molecular structure

The vibrational spectra of a solid crystalline sample of 2-biphenylmethanol have been measured at room temperature. The IR absorption spectra were recorded in the range 400 cm^–1–3600 cm^–1; Raman spectra were measured in the range 10 cm^–1–1640 cm^–1. The direct mechanical and optoelectronic problems were solved using the fragment method realized as Lev-100 software; the intensity distribution in the IR spectrum of 2-biphenylmethanol was obtained by the same method. The experimental Raman and IR absorption spectra were interpreted by analyzing the calculated data on the frequencies and forms of normal vibrations and their intensities in the IR spectra. IR absorption spectra were simulated for several models of 2-biphenylmethanol conformers that differ in the mutual orientation of fragments. Based on the results of simulation and comparison of the calculated and experimental spectra of conformers we suggested a model for the conformer realized in the solid phase under normal conditions.Original Russian Text Copyright © 2004 by L. M. Babkov, J. Baran, N. A. Davydova, J. I. Kukielskii, and S. V. TrukhachevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 624–631, July–August, 2004.This revised version was published online in April 2005 with a corrected cover date.     

Specific intermolecular interactions in a heterogeneous system benzophenone-titanium dioxide

IR spectroscopy methods (experiment, theoretical simulation) have been applied to study the structural features and intermolecular interactions in a two-component heterogeneous nano-size system benzophenone-titanium dioxide (BPh-TiO₂). IR spectra of the sample were recorded at room temperature within the range 400–4000 cm^?1. The spectra display hydrogen bonding determining the intermolecular interactions between titanium dioxide, BPh molecules, and water in the near-surface layers of nanocrystalline TiO₂ particles. IR spectra of free BPh molecules, water, model H-complexes of BPh with water, and the fragment of hydrated titania surface (BPh…HOH and BPh…Ti≡) have been simulated. Experimental and theoretical spectra were analyzed in the region of stretching vibrations of carbonyl, hydroxyl, and other groups sensitive to a variation of intermolecular interactions. It is found that hydrogen bonding in the near-surface layers of nanocrystalline TiO₂ particles in the two-component heterogeneous nanosystem BPh-TiO₂ gives rise to the formation of complexes BPh-O-Ti(OH)-O-, BPh…HOH, along with complexes of-O-Ti(OH)-O-with water and pure water complexes.     

The effect of the hydrogen bonds on the molecule conformation in 2-biphenylmethanol

Infrared spectra of hydrogen-bonded organic compound 2-biphenylmethanol has been studied in the wide temperature range from 320 to 12 K. It has been found that IR spectra drastically changed with temperature in the 700–850, 1290–1500, and 3100–3600 cm⁻¹ spectral regions, where deformational vibrations of phenyl rings and methanol group, as well as ν(OH) stretching vibration manifest themselves. The analysis of the computer simulation of the IR spectra for various 2-biphenylmethanol conformers, which are characterized by different combinations of angles of the mutual orientation of the phenyl rings relative to each other and a methanol group relative to the phenyl ring allowed us to conclude that the hydrogen bonding results not only in the shortened of the intermolecular bonds, but also in the increasing of the angle between phenyl ring and methanol group. In other words, hydrogen bonding leads to the changes in the molecule conformation.     

三(4-硝基苯基)甲烷衍生物的结构和振动光谱的理论研究（英文）

用密度泛函理论优化了三苯甲烷(1)和一系列三(4-硝基苯基)甲烷衍生物2,3和4的几何结构,并计算了其红外光谱和拉曼光谱;通过与实验光谱的对比,对实验光谱中的谱峰进行了指认,并从理论上纠正了部分对3和4红外光谱谱峰不合适的实验指认;同时预测了2,3和4的拉曼光谱.结果表明,几种化合物的振动光谱计算结果与相应的实验结果吻合良好;且化合物2,3和4的拉曼光谱具有相似性.     

Crystal and molecular structure of (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide

Crystal and molecular structure of a new homodrimanic compound (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide has been determined by X-ray diffraction analysis. The crystal is monoclinic, unit cell parameters are: a = 9.577(2) Å, b = 7.414(1) Å, c = 16.856(3) Å; β = 94.83(3)°, space group P2₁, Z = 2, of composition C₂₀H₃₅N₃O₂S. Two cyclohexan fragments have ordinary structure and chair-configuration typical of this compound class in homodrimanic skeleton. Ethanol molecule is located in the outer sphere. The withdrawal of carbon atoms from planar fragments of cyclohexan rings varies within the limits from 0.722(5) Å to − 0.634(5) Å. A dihedral angle between the mean-square planes of the latter equals 16.0(2)°, torsion angle (5)-(5)-(10)-(16) 171.0(1)° indicates their trans-joint. In the side non linear chain allyl group is connected to terminal nitrogen atom of thiosemicarbazide molecule. Intermolecular hydrogen bonds between carbonyl atom of acetamide fragment, ethanol molecule, and donor-acceptor groups of thiosemicarbazide moiety play the main part in crystal structure organization. Original Russian Text Copyright ? 2005 by E. P. Styngach, S. T. Malinovskii, L. P. Bets, L. A. Vlad, M. Gdanets, and F. Z. Makaev __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 46, No. 4, pp.785–789, July–August, 2005.     

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.     

Defective disordered crystal structure of (2-hydroxyphenyl)diphenylphosphineoxide

A disordered defective crystal structure of (2-hydroxyphenyl)diphenylphosphineoxide (I) has been studied by XRD method. The rhombic structure of I (space group Pna2₁, a = 18.271 Å, b = 8.337 Å, c = 19.629 Å, Z = 8) was solved by a direct method and refined by a full-matrix LSM having taken into account its crystal packing defects (by introducing two additional independent low-populated molecules) to R = 0.060 for all 3517 independent reflections measured (a CAD-4 autodiffractometer, λMoK _α. There are two independent molecules A and B with population 0.90 and two additional independent molecules C and D with population 0.10 in the structure of I.     

Synthesis and crystal structure of EnH<Superscript>2</Superscript>[IrCl<Superscript>6</Superscript>]

The preparation of EnH²[IrCl⁶] is described. Crystal data for C₂H₁₀Cl₆IrN₂ are: a = 6.8972(11) Å, b = 6.9435(16) Å, c = 7.3354(11) Å; α = 88.269(3)°, β = 65.495(2)°, γ = 60.305(2)°, V = 270.76(9) ų, space group P1, Z = 1, d_calc = 2.864 g/cm³. Crystal chemical analysis of the general motif of the structure was performed by the translation sublattice identification technique. It has been found that complex anions [IrCl₆]^2? follow the nodes of a rather regular rhombohedral subcell with the parameters a_c = 7.1 Å, α_c = 64°.     

Theoretical and experimental study of the adsorption of neutral glycine on silica from the gas phase.

The adsorption of neutral glycine onto amorphous silica was investigated both theoretically and experimentally. DFT calculations were performed at the BLYP-631++G** level using a cluster approach. Several possible configurations involving the formation of H bonds between glycine and one, two, or three silanol groups (SiOH) were considered. The most favorable bonding of glycine with one silanol group (45 kJ mol(-1)) occurs through the COOH moiety, thus forming a cycle in which the CO group is an H-bond acceptor whereas the acidic OH group is an H-bond donor. With two or three silanol groups, additional H bonds are formed between the amine moiety and the silanol groups, which leads to an increased adsorption energy (70 and 80 kJ mol(-1) for two and three silanol groups, respectively). Calculated nu(CO), delta(HNH), and delta(HCH) values are sensitive to the adsorption mode. A bathochromic shift of nu(CO) as compared to the nu(CO) of free glycine (calculated in the 1755-1790 cm(-1) range) is found for glycine in interaction with silanol(s). The more H bonds are formed between the COOH moiety and silanol groups, the higher the bathochromic shift. For delta(HNH), no shift is found for glycine adsorbed on one and two silanol groups (where the amine is either not bound or an H-bond donor), whereas a bathochromic shift is calculated with three silanols when the amine moiety is an H-bond acceptor. Experimental FTIR spectra performed at room temperature for glycine adsorbed at 160 degrees C on Aerosil amorphous silica exhibit bands at 1371, 1423, 1630, and 1699 cm(-1). The experimental/calculated frequencies have their best correspondence for glycine adsorbed on two silanol groups. It is important to note that the forms giving the best correspondence to experimental frequencies are the most stable ones.     

The role of hydroxyl groups in interchain interactions in cellulose Iα and Iβ

Complex networks of hydrogen bonds within the cellulose I_α and I_β contribute greatly to cellulose's anisotropic physical properties such as material stiffness. The interchain hydrogen bonding interactions through hydroxyl groups are isolated in each of the three lattice planes of the adjacent chains within the unit cell of two allomorphs of natural cellulose. In our density function theory study with dispersion corrected Perdew–Burke–Ernzerhof (PBE‐D2) functional, these hydroxyl groups participate in strong hydrogen bonding interactions (?24.8 and ?24.8 kcal/mol for cellulose I_α and I_β, respectively) in the side‐to‐side lattice plane. Unexpectedly, the hydroxyl groups also participate significantly in hydrogen bonding interactions (?11.0 and ?12.4 kcal/mol for cellulose I_α and I_β, respectively) in one of the diagonal lattice planes in both cellulose I_α and I_β. Both PM7 and PBE‐D2 method predict that the overall interaction is asymmetric and stronger in the right diagonal lattice plane. While hydrogen bonding interactions are strongest in side‐to‐side lattice plane as expected, the role of hydrogen bonding interactions for keeping the sheet together is more significant than previously thought.     

Crystal and molecular structure of N-(benzylimidazolyl-2)-O-methylcarbamate salts

Single crystal X-ray diffraction has been applied to determine the structure of salts — formate and hydrochloride of N-(benzylimidazolyl-2)-O-methylcarbamate (BMC). The crystal structure of BMC formate is built by a molecule of a base and two formic acid molecules, one of them protonating a BMC molecule. Hydrogen bonds in the crystal form a weakly bound one-dimensional ribbon. BMC hydrochloride crystallizes as dihydrate. Two molecules of crystallization water and Cl ion make a robust H-bonded two-dimensional layer. BMC salts are formed through the protonation of N9 atom.     

Computer simulation and diffraction studies of the structure of liquid benzene

The review offers critical analysis of the results of the diffraction studies and computer simulation of the structure of liquid benzene. It is shown that until recently, structural studies were mainly investigations of the nearest surroundings of molecules, but did not ultimately provide reliable data. Modern approaches to studies of liquids at higher levels are considered, and a structural model of liquid benzene is suggested.     

Dissecting Noncovalent Interactions in Carboxyl-Functionalized Ionic Liquids Exhibiting Double and Single Hydrogens Bonds Between Ions of Like Charge

We show that the carboxyl-functionalized ionic liquid 1-(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC-CH₂-py][NTf₂] exhibits three types of hydrogen bonding: the expected single hydrogen bonds between cation and anion, and, surprisingly, single and double hydrogen bonds between the cations, despite the repulsive Coulomb forces between the ions of like charge. Combining X-ray crystallography, differential scanning calorimetry, IR spectroscopy, thermodynamic methods and DFT calculations allows the analysis and characterization of all types of hydrogen bonding present in the solid, liquid and gaseous states of the ionic liquid (IL). We find doubly hydrogen bonded cationic dimers (c⁺=c⁺) in the crystalline phase. With increasing temperature, this binding motif opens in the liquid and is replaced by (c⁺−c⁺−a⁻ species, with a remaining single cationic hydrogen bond and an additional hydrogen bond between cation and anion. We provide clear evidence that the IL evaporates as hydrogen-bonded ion pairs (c⁺−a⁻) into the gas phase. The measured transition enthalpies allow the noncovalent interactions to be dissected and the hydrogen bond strength between ions of like charge to be determined.     

Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99, -16.73 and -15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes. The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet （n,n＊） vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.     

金属皂的晶体结构

钠、钾以外金属的高级脂肪酸盐通称金属皂。它们兼具金属盐和脂肪酸的特性,在工业上广泛用作为塑料助剂(热稳定剂、润滑剂等)、油漆催干剂、增稠剂、防水剂、脱模剂,爽滑剂等[1]。金属皂的许多特性随脂肪链长度和金属种类的不同而变化。稀土、碱土和锌、镉、铅等金属皂是重要的PVC热稳定剂和润滑剂[2,3]。前文[4,5]已报道了稀土金属皂结构的红外光谱和X 射线衍射谱,本文报道镁、钙、锶、钡、锌、镉、铅与棕榈酸、肉豆蔻酸、月桂酸、癸酸锌、辛酸形成金属皂结构的X 射线衍射谱。1　实验部分1 1　金属皂合成采用复分解法[1]合成,产物均…     

Crystalline and molecular structures of two halogenated propionamides CF2XCF2CONH2 (X = H, Cl)

Using the XRD method, the crystalline and molecular structures of two halogenated propionamides, CF₂XCF₂CONH₂, X = H (I) and Cl (II), have been studied. Crystals I and II are monoclinic: space group P2₁/c, Z = 4; (I) a = 10.967 Å, b = 5.406 Å, c = 10.063 Å, β = 107.86°; (II) a = 11.979 Å, b = 5.608 Å, c = 10.042 Å, β = 99.31°. Structures I and II were solved by the direct method and refined by the full-matrix least-square method to R = 0.112 (I) and 0.139 (II) over all 1299 (I) and 1175 (II) independent measured reflections (a CAD-4 autodiffractometer, λMoK _α).