聚乙烯唑啉作用下甲烷水合物分解的分子动力学模拟

利用分子动力学模拟系统研究了不同质量浓度下(1.25%、2.50%、6.06%)聚乙烯唑啉(PEtO)对甲烷水合物的分解作用. 模拟体系为甲烷水合物2′2′2的超胞和聚合物对接体系. 模拟发现水分子间氢键构架的水合物笼型结构在PEtO的作用下出现扭曲, 最终导致水合物笼型结构完全坍塌. 通过氧原子径向分布函数、均方位移以及扩散系数比较不同浓度PEtO的作用, 证实在一定浓度范围内, PEtO的浓度越高, 其水合物分解作用越强. 此外, PEtO 具有一定的可生物降解性. PEtO 对水合物的作用为: PEtO 吸附在水合物表面, 其中的酰胺基(N―C＝O)与成笼的水分子形成氢键, 破坏邻近的笼形结构, 令水合物分解; PEtO不断分解表面的水合物, 直到水合物笼完全分解.     

Effect of compression on interaction between 1,4-dihydropyridine compounds and lactose monohydrate

Manidipine dihydrochloride or benidipine hydrochloride will change to hydrate form in part, when differential scanning calorimetric (DSC) measurement is carried out together with lactose monohydrate. This interaction was accelerated by compressing their mixture. It can be suggested that the interaction may cause by the disruption of crystal structure of lactose monohydrate due to compression to set free of water molecules. A new DSC peak at 170 degrees C, which was not observed in each component, appeared in DSC measurement of a mixture. This will be based on hydrate formed by the interaction, i.e., movement of water molecules. The profile of the plotting of the DSC peak area ratio before and after compression against the compression force changed by the molar ratio of lactose monohydrate in a mixture. In the case of low molar ratio of lactose monohydrate, profiles for manidipine dihydrochloride and benidipine hydrochloride differed from each other. This will be because manidipine dihydrochloride is stickier than benidipine hydrochloride. The profile for manidipine dihydrochloride became more gradual and showed lag compression force region when the amount of addition of the lubricant, magnesium stearate in a mixture increased. The endothermic peak area at 170 degrees C for manidipine dihydrochloride was larger than that for benidipine hydrochloride. It should be suggested that benidipine hydrochloride is easier to be transformed to its hydrate than manidipine dihydrochloride.     

Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

The structure of water in p-sulfonatocalix[4]arene

Tetrasodium p-sulfonatocalix[4]arene exists as a hydrate with approximately 14 water molecules and has three polymorphic modifications, all of which contain a water molecule in the molecular cavity that is engaged in OH···π interactions. Single-crystal neutron structures are reported for two of these three forms and reveal a "compressed" water molecule with short OH bonds. Partial atomic charges and hardness analysis (PACHA) calculations based on the neutron coordinates give an OH···π interaction energy of 6.9-7.5 kJ mol(-1). The PACHA analysis also reveals the dominance of the charge-assisted hydrogen bonds from the Na(+)-coordinated water molecules. The instability of the crystal towards dehydration can be traced to an uncoordinated lattice water site. The remarkable calixarene-Na(+)-hydrate motif is conserved almost unchanged across all three polymorphs. A single-crystal neutron structure is also reported for pentasodium p-sulfonatocalix[4]arene·12H(2)O, which exhibits an intracavity water molecule that is engaged in both OH···π and OH···O hydrogen bonding. The shorter covalent bond to the hydrogen atom that forms the interaction with the aromatic ring is again apparent.     

dl‐Alaninium semi‐oxalate monohydrate

The structure of the title compound, C₃H₈NO₂⁺·C₂HO₄⁻·H₂O, is formed by two chiral counterparts (l ‐ and d ‐alaninium cations), semi‐oxalate anions and water molecules, with a 1:1:1 cation–anion–water ratio. The structure is compared with that of the previously known anhydrous dl ‐alaninium semi‐oxalate [Subha Nandhini, Krishnakumar & Natarajan (2001). Acta Cryst. E 57 , o666–o668] in order to investigate the role of water molecules in the crystal packing. The structure of the hydrate resembles that of anhydrous alaninium semi‐oxalate, with the water molecule incorporated into the general three‐dimensional network of hydrogen bonds where it forms four hydrogen bonds with neighbours disposed tetrahedrally about it. Although the main structural motifs in the hydrate and in the anhydrous form are topologically similar, the incorporation of water molecules in the network results in significant geometric distortion. There are several types of hydrogen bond in the crystal structure of the hydrate, two of which (O—H...O bonds between the semi‐oxalate anions and O—H...O hydrogen bonds between water and alaninium cations) are very short. Such hydrogen bonds between semi‐oxalate anions are also present in the anhydrous form of this compound. Short distances between semi‐oxalate anions in neighbouring chains in the hydrate alternate with longer ones, whereas in the anhydrous structure they are equidistant. Despite the similarity of these compounds, dehydration of the hydrate on storage is not of a single‐crystal to single‐crystal type, but gives a polycrystalline pseudomorph, preserving the crystal habit. This transformation proceeds through the formation of an intermediate compound, presumably a hemihydrate.     

甘油对冰晶生长抑制作用的分子动力学模拟

采用分子模拟方法研究了正交晶系冰晶(020)生长面在不同浓度甘油水溶液中的生长情况. 通过统计分析氢键数、 密度分布函数、 均方根偏差和原子间径向分布函数研究了水分子和甘油分子的动态行为. 结果表明, 甘油分子在水溶液中可与水分子形成大量氢键, 这使水分子间的氢键作用受到抑制, 降低了水分子的扩散性, 致使冰晶不易成核和生长; 另外, 一些甘油分子可代替水分子吸附在晶面上, 甚至占据晶格位点, 这种行为打破了冰晶的对称性并且降低了冰晶的生长速率. 因此, 甘油可同时在晶面和液相中抑制冰晶的生长.     

Effect of small cage guests on hydrogen bonding of tetrahydrofuran in binary structure II clathrate hydrates

Molecular dynamics simulations of the pure structure II tetrahydrofuran clathrate hydrate and binary structure II tetrahydrofuran clathrate hydrate with CO(2), CH(4), H(2)S, and Xe small cage guests are performed to study the effect of the shape, size, and intermolecular forces of the small cages guests on the structure and dynamics of the hydrate. The simulations show that the number and nature of the guest in the small cage affects the probability of hydrogen bonding of the tetrahydrofuran guest with the large cage water molecules. The effect on hydrogen bonding of tetrahydrofuran occurs despite the fact that the guests in the small cage do not themselves form hydrogen bonds with water. These results indicate that nearest neighbour guest-guest interactions (mediated through the water lattice framework) can affect the clathrate structure and stability. The implications of these subtle small guest effects on clathrate hydrate stability are discussed.     

Formation of a hydrogen-bonded heptazine framework by self-assembly of melem into a hexagonal channel structure

Self-assembly of melem C(6)N(7)(NH(2))(3) in hot aqueous solution leads to the formation of hydrogen-bonded, hexagonal rosettes of melem units surrounding infinite channels with a diameter of 8.9 ?. The channels are filled with strongly disordered water molecules, which are bound to the melem network through hydrogen bonds. Single-crystals of melem hydrate C(6)N(7)(NH(2))(3)?xH(2)O (x≈2.3) were obtained by hydrothermal treatment of melem at 200 °C and the crystal structure (R ?3c, a=2879.0(4), c=664.01(13) pm, V=4766.4(13)×10(6) pm(3), Z=18) was elucidated by single-crystal X-ray diffraction. With respect to the structural similarity to the well-known adduct between melamine and cyanuric acid, the composition of the obtained product was further analyzed by solid-state NMR spectroscopy. Hydrolysis of melem to cyameluric acid during syntheses at elevated temperatures could thus be ruled out. DTA/TG studies revealed that, during heating of melem hydrate, water molecules can be removed from the channels of the structure to a large extent. The solvent-free framework is stable up to 430 °C without transforming into the denser structure of anhydrous melem. Dehydrated melem hydrate was further characterized by solid-state NMR spectroscopy, powder X-ray diffraction, and sorption measurements to investigate structural changes induced by the removal of water from the channels. During dehydration, the hexagonal, layered arrangement of melem units is maintained whereas the formation of additional hydrogen bonds between melem entities requires the stacking mode of hexagonal layers to be altered. It is assumed that layers are shifted perpendicular to the direction of the channels, thereby making them inaccessible for guest molecules.     

Solid-state NMR and calorimetry of structural waters in helical peptides

The peptide hydrates Gly-Gly-Val x 2H(2)O (GGV) and Gly-Ala-Leu x 3H(2)O (GAL) are known to adopt alpha-helical configurations containing waters of hydration in which each water is H-bonded to three or four peptide groups. Herein we report a thermodynamic and solid-state NMR ((2)H and (17)O) study of these peptides. From TGA and DSC, the average enthalpy per H-bond is 15 kJ/mol. The dynamics and average orientation of the hydrate are studied by powder and single-crystal (2)H NMR. Whereas waters that are shown by the X-ray structure to be coordinated by four hydrogen bonds do not yield observable (2)H NMR signals at room temperature, two of the three triply coordinated waters yield residual (2)H quadrupole coupling tensors characteristic of rapid 180 degrees flip motions and the orientation of the residual tensor is that expected from the X-ray structure-derived H-bonding pattern. At -65 degrees C, the flip motions of triply coordinated water in GGV slow into the (2)H NMR intermediate exchange regime whereas the tetrahedrally coordinated water approaches the slow-exchange limit and yields an observable NMR signal. Extensive isotope exchange between water vapor and crystalline GGV establishes the presence of additional hydrate dynamics and solid-state proton transfer along a chain of water-bridged protonated alpha-amino groups.     

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO(2) molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.     

A Model System for the Study of Competitive Coordination in Aminoheterocyclic Complexes. Molecular and Crystal Structure of 2-Amino-1-methyl-Benzoimidazolium Chloride Hydrate

2-Amino-1-methyl-benzoimidazolium chloride hydrate was structurally characterized by X-ray diffraction analysis. Its crystal is built from organic cations, chloride anions, and molecules of crystallization water, which are united through a related system of hydrogen bonds. In the organic cation, the proton is localized at the N atom of the pyridine type.     

Two-dimensional infrared spectroscopy study on phase transition and structural variations of a hydrogen-bonded liquid crystal

Infrared (IR) spectra have been measured for a liquid crystal (LC) consisting of one trans-butene diacid (BD) molecule as a proton donor and two 4-(2,3,4-tridecyloxybenzoyloxy)-4'-stilbazoles (DBS) molecules as a proton acceptor (DBS:BD:DBS) linked together with each other by inter-molecular hydrogen bonds over a temperature range from 20 to 120 degrees C to explore its phase transition and heat-induced structural variations. The temperature-dependent IR spectra have shown that the inter-molecular hydrogen bonds are stable in the liquid crystalline phase but become slightly decoupled with temperature increasing. Two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations more efficiently. The SS 2D correlation analysis in the spectral range of 2700-1800 cm(-1) has demonstrated that a change in hydrogen bonds in the LC starts from 40 degrees C, which is not clarified by differential scanning calorimetry (DSC) and conventional IR and Raman spectroscopic analyses. On the other hand, the phase transition of LC revealed by SS 2D spectroscopy in the specific spectral regions of 1750-1650 and 3000-2700 cm(-1) is in a good agreement with that revealed by DSC for the heating process. The VV 2D correlation spectroscopy analysis has provided information about the structural variations of inter-molecular hydrogen bonds. The different species of hydrogen-bonded and free -COOH and -COO- groups in the LC have been clarified by the VV 2D correlation analysis. It has also elucidated the specific order of the temperature-induced structural changes in the intra- and inter-molecular hydrogen bonds concerning with the -COOH and/or -COO- groups in the LC.     

Effects of dehydration temperatures on moisture absorption and dissolution behavior of theophylline.

Anhydrous theophylline was prepared by heating theophylline monohydrate at temperatures between 60 degrees C and 140 degrees C. The effects of dehydration temperatures on the moisture absorption and dissolution behavior of anhydrous theophylline were investigated in this study. The hydration rate of anhydrous theophylline at 95% relative humidity and 25 degrees C decreased with increasing dehydration temperatures. From the fitting analysis of solid-state reaction models, the hydration reaction was found to be governed by the phase boundary reaction model for samples prepared at lower dehydration temperatures (<100 degrees C) but the reaction obeyed the growth of nuclei reaction model when samples were dehydrated at higher temperatures. The dissolution rates of various anhydrous theophylline samples were measured by the rotating disk method. The calculated solubility of anhydrous theophylline prepared by heating was about 2.5 times higher than that of theophylline monohydrate. The phase transformation rate from the anhydrous form to the monohydrate during dissolution tests decreased with higher dehydration temperatures. It was found that the anhydrous theophylline prepared at different dehydration temperatures transformed to the monohydrate by way of different growth of hydrate nuclei mechanism.     

Structural features and N-H…O and O-H…O hydrogen-bonded supramolecular frameworks in 2-methylanilinium hydrogen DL-malate hydrate, 4-methoxyanilinium and 4-methylanilinium hydrogen DL-malate salts

In the crystal structure of 2-methylanilinium hydrogen DL-malate hydrate (I), an additional water molecule is present in asymmetric unit. In the crystal structures of 4-methoxyanilinium hydrogen DL-malate (II) and 4-methylanilinium hydrogen DL-malate (III), the hydrogen malate anions exhibit configurational disorder with major component occupy S-configuration and minor component occupy R-configuration provided both (II) and (III) are prepared from a racemic mixture of DL-malic acid. In crystal structures of compounds (I)–(III), the hydrogen malate anions and anilinium cations from O-H…O and N-H…O hydrogen bonds which exhibit interesting supramolecular frameworks. In compound (I), the N-H…O and O-H…O hydrogen-bonded anionic-cationic framework form two-dimensional hydrophilic and hydrophobic layers in which the lattice water molecules are embedded in hydrophilic layers. However, in crystal structures of (II) and (III), the hydrogen DL-malate anions form two-dimensional anionic substructure through O-H…O hydrogen bond, in which the anilinium cations are anchored through N-H…O hydrogen bonds.

     

Influence of structure of the crystal lattice of nickel(II) complex with amide-containing ligand on its stability and adsorption properties

The characteristic of the crystal lattice of the hydrate of a nickel complex with a tetradentate amide-containing ligand is the presence of hexamers of the metal complex molecule, united by intermolecular hydrogen bonds which are retained during adsorption and desorption of polar molecules. The lattice of this material is characterized by a definite lability which arises during interaction with methanol. __________ Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 43, No. 1, pp. 47–51, January–February, 2007.     

Comparative study of the hydration systems formed during interactions of hydrogen phosphate dianions with putrescine, nor-putrescine and magnesium dications

A comparative study of hydration systems, formed as a result of the interaction between hydrogen phosphate dianions and three naturally occurring cations (putrescine (Put), its nor-homologue (nPut) and magnesium), is presented. On the basis of X-ray data and IR, NMR and calorimetric measurements, we have determined how the structure and physicochemical properties of the cations influence the system of phosphate residue hydration. Our study demonstrates that the stability of the hydration systems depends not only on the character of the bonds used by water to link with other salt components (coordinate or hydrogen bonds), but also on the location of the water molecules in the crystal lattice. In addition, contrary to magnesium salts, the dehydration of diamine (Put and nPut) hydrogen phosphates is reversible. Both dehydration and rehydration processes take place in the solid state. During rehydration, the crystalline anhydrous salt absorbs water molecules from the atmosphere. This leads to the reconstruction of the hydrated salt structure; this means that the salt which is the product of rehydration is identical with that obtained by crystallization from water solution.     

Effect of the orientation of the water molecules in the system of hydrogen bonds in the crystal hydrate of m-bromo-N′-(5-nitrofurylidene)benzohydrazide on its sensitivity to light

On the basis of a crystal-chemical analysis of the structure of the investigated benzohydrazides, the structural characteristics typical of light-sensitive crystal hydrates of this type were formulated: the formation of intermolecular polar chains of hydrogen bonds of the C=O...H₂O...H-N type with the water molecules; head-to-tail stacking of the molecules. It was shown that the investigated m-bromo-N-(5-nitrofurylidene)benzohydrazide forms 12 crystal hydrates. The dimeric associates of the water molecules link the benzohydrazide molecules in the stacks by hydrogen bonds. Polar chains of hydrogen bonds, along which intermolecular N O-phototransfer of a proton occur, are formed between the stacks with the participation of one of the water molecules. An assignment was made of the bands for the OH stretching vibrations of the water molecules in the investigated crystal hydrate.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 567–572, March, 1990.     

常见客体分子对笼型水合物晶格常数的影响

Natural gas hydrates are considered as ideal alternative energy resources for the future, and the relevant basic and applied research has become more attractive in recent years. The influence of guest molecules on the hydrate crystal lattice parameters is of great significances to the understanding of hydrate structural characteristics, hydrate formation/decomposition mechanisms, and phase stability behaviors. In this study, we test a series of artificial hydrate samples containing different guest molecules (e.g. methane, ethane, propane, iso-butane, carbon dioxide, tetrahydrofuran, methane + 2, 2-dimethylbutane, and methane + methyl cyclohexane) by a low-temperature powder X-ray diffraction (PXRD). Results show that PXRD effectively elucidates structural characteristics of the natural gas hydrate samples, including crystal lattice parameters and structure types. The relationships between guest molecule sizes and crystal lattice parameters reveal that different guest molecules have different controlling behaviors on the hydrate types and crystal lattice constants. First, a positive correlation between the lattice constants and the van der Waals diameters of homologous hydrocarbon gases was observed in the single-guest-component hydrates. Small hydrocarbon homologous gases, such as methane and ethane, tended to form sI hydrates, whereas relatively larger molecules, such as propane and iso-butane, generated sⅡ hydrates. The hydrate crystal lattice constants increased with increasing guest molecule size. The types of hydrates composed of oxygen-containing guest molecules (such as CO₂ and THF) were also controlled by the van der Waals diameters. However, no positive correlation between the lattice constants and the van der Waals diameters of guest molecules in hydrocarbon hydrates was observed for CO₂ hydrate and THF hydrate, probably due to the special interactions between the guest oxygen atoms and hydrate "cages". Furthermore, the influences of the macromolecules and auxiliary small molecules on the lengths of the different crystal axes of the sH hydrates showed inverse trends. Compared to the methane + 2, 2-dimethylbutane hydrate sample, the length of the a-axis direction of the methane + methyl cyclohexane hydrate sample was slightly smaller, whereas the length of the c-axis direction was slightly longer. The crystal a-axis length of the sH hydrate sample formed with nitrogen molecules was slightly longer, whereas the c-axis was shorter than that of the methane + 2, 2-dimethylbutane hydrate sample at the same temperature.     

Polarized vibrational studies of bisguanidinium hydrogenphosphate monohydrate

Detailed vibrational studies (FTIR and Raman on powder samples, polarized FTIR microscope on a small single crystal, polarized FTIR using Bruker reflection unit on a single crystal and polarized Raman) have been carried out. Vibrational spectra are discussed in relation to the crystal structure published previously. In this crystal a network of hydrogen bonds link water molecules, guanidinium cations and hydrogenphosphate ions. The 13 different hydrogen bonds in G2HP crystal structure are detected. On the basis of detailed vibrational studies the detailed assignment of observed bands was made. Calorimetric (DSC) studies have been performed, but no phase transition was found in the temperature range 100-350 K.     

The system of hydrogen bonds in Ba2Re6Te8(CN)6·12H2O: Simulation and NMR study

The crystal hydrate Ba₂Re₆Te₈(CN)₆· 12H₂O whose structural fragments are the cluster onions [Ba₂Re₆Te₈(CN)₆]^4? is studied by¹H NMR. In the triclinic cell (space group P-1), the barium atoms coordinated by six water molecules are united into the dimers [Ba· 5H₂O] ₂ ⁴⁺ by two bridging H₂O molecules; the water molecules lying outside the coordination sphere of Ba are located in the structure channels running along the [001] direction. Diffusion of H₂O molecules was found in the range of temperatures 100?C below the temperature of intense dehydration of the crystal. The structure of the water lattice of the compound is modeled by calculating Coulomb interactions between hydrogen and surrounding atoms and analyzing the NMR spectra recorded under translational diffusion conditions for H₂O. Half of the protons in H₂O molecules are involved in the formation of hydrogen bonds whose lengths lie within 2.78–2.86 å (O-H…O) and 2.92-3.13 å (O-H…N). The water lattice structure is preserved up to ≈100?C. The water subsystem is radically rearranged upon subsequent heating followed by partial dehydration of the crystal.