Molecular clusters in aqueous solutions of pyridine and its methyl derivatives

Small-angle neutron scattering proved that molecules in aqueous solutions of pyridine, 2-methylpyridine and 2,6-dimethylpyridine form clusters. The clusters are dynamic aggregates consisting of hydrogen-bonded water-amine complexes. Strengthening of the hydrogen bonds between water and amine molecules due to the methyl groups in the ortho position in the pyridine ring makes the structures more stable, as was evidenced by relatively long times of the structural relaxation. The strong intermolecular forces affect the thermal expansion of the systems. No aggregates similar to those in aqueous systems are present in the methanolic ones. That points to the crucial role of water in the molecular clustering. A molecule of methanol, although capable of hydrogen bonding with the amines, cannot participate in larger structures because of the lack of protons that could form the enhanced network. Thus, even if the amine-methanol complexes occur, they are incapable of further association. It was shown that the co-operative nature of hydrogen bonds and the propensity of water to association are the main factors that determine the properties of aqueous systems.     

Structure and dynamics of water in mixed solutions including laponite and PEO

To investigate the structure and dynamics of water in mixed solutions including laponite clay particles and poly(ethylene oxide) (PEO), we measured the Raman spectra of the mixed solutions in the temperature range 283-313 K. The results show that the vibrational energies of the O-H stretching modes in the mixed solutions depend on the water content and temperature. The energy shifts of the O-H stretching modes are attributed to changes in the water structure. By applying a structural model of bulk water to the spectra in the O-H stretching region, the local structures of water in the solutions were analyzed. The result shows that the formation probability of hydrogen bonds in the solutions decreases as the water content decreases. Laponite and PEO have effects to disrupt the network structure of hydrogen bonds between water molecules. Further, it was found that laponite and PEO cause increase in the strength of hydrogen bonds of surrounding water,although the strength of the hydrogen bonds increases with the order water-laponite < water-water < water-PEO. It is concluded that water in laponite-PEO mixed solutions has a less-networked structure with strong hydrogen bonds compared with bulk water.     

An intermediate radial distribution curve maximum of water and its relation to the topology of the network of H-bonds in liquid water

The structure of a complex of a water molecule with first and second coordination sphere molecules was analyzed. Model structures were calculated using the TIP3P and Poltev-Malenkov potentials. It was found that stable structures of four water molecules could exist. In these structures, oxygen atoms are situated at characteristic distances of 0.37 nm from each other. This distance corresponds to the “intermediate” maximum of the radial distribution curve. The existence of such structures correlates with the formation of bifurcated bonds in liquid water. This result can be obtained by changing the topology of the water structure while retaining the tetrahedral character of structural elements.     

Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates

Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the “suprastructures” typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer “gc” and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.     

Structural correlations in liquid water: a new interpretation of IR spectroscopy

We present a new and alternative interpretation of the structure of the IR vibrational mode (nu(OH) band) of pure water. The re-interpretation is based on the influence of the cooperative hydrogen bonding arising from a network of hydrogen bonds in the liquid. The nu(OH) band has six components that are dominated by differences in their O-H bond lengths but deviate from thermodynamically average values due to interactions with the hydrogen bond network. The physical origin of the structure in the nu(OH) band is directly related to the O-H bond length, and variations in this bond length are caused by the influence of the surrounding hydrogen-bonded network of water molecules.     

Properties of the network of the hydrogen bonds of water

Networks of the hydrogen bonds and those consisting of lines connecting nearby molecules were constructed using configurations of water molecules obtained by the Monte-Carlo method. The concentrations of closed cycles of hydrogen bonds were established to be determined only by the probability of hydrogen bond formation. Characteristics of a model ideal water network were determined. Topological properties of the Polk model and those of the network of nearest neighbors substantially differ from the properties of the ideal network. The totality of the hydrogen bonds in pure water was proposed to be considered as a hierarchical system. Three topologically different structures of water associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 928–931, May, 1997.     

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

Ultrafast structural dynamics of water induced by dissipation of vibrational energy

In the liquid phase, water molecules form a disordered fluctuating network of intermolecular hydrogen bonds. Using both inter- and intramolecular vibrations as structural probes in ultrafast infrared spectroscopy, we demonstrate a two-stage structural response of this network to energy disposal: vibrational energy from individually excited water molecules is transferred to intermolecular modes, resulting in a sub-100 fs nuclear rearrangement that leaves the local hydrogen bonds weakened but unbroken. Subsequent energy delocalization over many molecules occurs on an approximately 1 ps time scale and is connected with the breaking of hydrogen bonds, resulting in a macroscopically heated liquid.     

甘油水溶液氢键特性的分子动力学模拟

为了研究低温保护剂溶液的结构和物理化学特性, 以甘油为保护剂, 采用分子动力学方法, 对不同浓度的甘油和水的二元体系进行了模拟. 得到了不同浓度的甘油水溶液在2 ns内的分子动力学运动轨迹, 通过对后1 ns内运动轨迹的分析, 得到了各个原子对的径向分布函数和甘油分子的构型分布. 根据氢键的图形定义, 分析了氢键的结构和动力学特性. 计算了不同浓度下体系中平均每个原子(O和H)和分子(甘油和水)参与氢键个数的百分比分布及其平均值. 同时还计算了所有氢键、水分子之间的氢键以及甘油与水分子之间的氢键的生存周期.     

Programmed construction of discrete self-assembled cyclic aggregates

Examples for programmed self-assembly of alpha,beta-unsaturated ketoximes carrying a terminal pyridine subunit are described. The solid-state structures of a series of pyridinyl alpha,beta-unsaturated ketoximes 1 were investigated by X-ray structural analysis; this demonstrated that molecules 3-5 predictably form discrete cyclic aggregates stabilized by a network of hydrogen bonds and aromatic interactions.     

Structural changes in water clusters during methane adsorption

The structure of water clusters that have adsorbed from one to six methane molecules is studied by molecular dynamics simulation. Characteristic structural units of Voronoi and hybrid polyhedra are employed to reveal the structural changes resulting from the attachment of CH₄ molecules to the clusters. The most significant changes in topological properties are associated with variations in the number of faces of simplified polyhedra. A change is unambiguously detected in the small-angle peak intensity in the angular distribution of nearest geometrical neighbors determined with the use of the Voronoi polyhedra. The results of two different calculations of the number of hydrogen bonds in the clusters are compared, and the “nonsphericity” coefficients are calculated for the polyhedra.     

Liquid structure of acetic acid-water and trifluoroacetic acid-water mixtures studied by large-angle X-ray scattering and NMR

The structures of acetic acid (AA), trifluoroacetic acid (TFA), and their aqueous mixtures over the entire range of acid mole fraction xA have been investigated by using large-angle X-ray scattering (LAXS) and NMR techniques. The results from the LAXS experiments have shown that acetic acid molecules mainly form a chain structure via hydrogen bonding in the pure liquid. In acetic acid-water mixtures hydrogen bonds of acetic acid-water and water-water gradually increase with decreasing xA, while the chain structure of acetic acid molecules is moderately ruptured. Hydrogen bonds among water molecules are remarkably formed in acetic acid-water mixtures at xA相似文献   

Zur Reaktionsweise von Enaminen mit Cyclopropenonen IV. Einsatz von Ketenacetalen

A new interpretation – based on a reevaluation of the spectroscopic properties of products 16 to 27 – is proposed for the reaction of diphenyl-cyclopropen-one 14 and -thione 15 with ketene-A, N-diacetals 8 to 13 (A ? R₂N, RO and RS) originally reported by Sauer & Krapf. It is concluded that the previous structural assignments (see the a-structures), made on the assumption of a prevailing “C,C-insertion” reaction, must be rcplaced as follows: (1) All the “secondary adducts” are, in fact, derivatives (amides and lactams) of 2,3-diphenyl-penta-2, 4-dienoic acid and thioacid (structures 16b to 24b ); (2) the “isomerization products”, differ from the latter only in the configuration of the α,β-double bond (structures 25b and 26b ); (3) the common “hydrolysisproduct” is α,β-diphenyl-γ-methyl-γ-hydroxy-Δ^α-butenolide ( 27b ), The above cyclopropenone-ketcneacetal reactions represent, therefore, cases of “C, N-insertion”. This is rationalized with a reaction scheme, in which the “acylide” structure of the “primary adducts” plays a role.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

A brief review on formation of (H2O)n clusters in supramolecular proton transfer compounds and their complexes

“Water clusters”, group of water molecules held together by hydrogen bonds, have been the subject of a number of intense experimental and theoretical investigations because of their importance in understanding cloud and ice formation, solution chemistry, and a large number of biochemical processes. “Water clusters” can play an important role in the stabilization of supramolecular systems both in solution and in the solid state and there is clearly a need for chemists a better understanding of how such aggregates influence the overall structure of their surroundings. The present brief review deals with (H₂O)_n clusters, identified/observed crystallographically upon 170 crystal structures of synthesized coordination compounds based upon proton transfer compounds by Hossein Aghabozorg’s research groups since 2000. The structural details of water clusters, (H₂O)_n, n = 2, 3, 4, 5, 6, 7, 8, 9, 15, 16 and ∞ are described systematically.     

Moleular simulation of surface reorganization and wetting in crystalline cellulose I and II

Cellulose is one of the most versatile substances in the world. Its immense variety of applications was in recent years complemented by nanotechnological applications such as cellulose nanoparticle dressed surfaces for filtration purposes or cellulose matrices for microelectronics. The fabrication of such complex materials asks for thorough understanding of the surface structure and its interactions with adsorbates. In this study we investigate several surface model systems of nanotechnological interest, which are obtained by reorganization of the cellulose-vacuum or cellulose-water interfaces of slabs of crystalline cellulose. To do this, we equilibrated first bulk supercells of different cellulose allomorphs, which were constructed from crystallographic data, and then optimized the interface structures. From the bulk and surface systems we calculated structural properties such as unit cell parameters, dihedral conformation distributions, density profiles and hydrogen bonding. The results suggest that no overall geometrical restructuring occurs at the interface. However, the hydrogen bond network is strongly reconstructed, as is inferred from the dihedral conformations and hydrogen bond occurrences, although only within the first few layers. This holds for low index close packed structures as well as for high index loosely packed surfaces. Replacing the vacuum by ambient pressure water molecules we find less rearrangements of the cellulose surface, because the water allows formation of hydrogen bonds similar to those in the bulk phase. The water near the cellulose surface shows, however, strong structural changes. We observe reduced mobility of the water molecules, which corresponds to a cooling of water by about 30°, in a slab that is about 10 Å thick. Although structuring and adsorption is observed on all surfaces, no actual penetration of water into the cellulose structure could be observed. This suggests that pure water is not sufficient to produce cellulose swelling at mesoscopic timescales. This work lays the basis for current quantum chemical investigations on specific interaction terms within cellulose.     

Structured water and water-polymer interactions in hydrogels of molecularly imprinted polymers

Recently, molecular imprinting technology has fleetly developed for applications in different fields. It shows great potential in sensor design, drug delivery, chromatography separation, catalysis, chiral synthesis, and especially in the molecular recognition field. In this work, a cubic model of a hydrogel network was developed and an infinite hydrogel backbone network was constructed for molecular dynamics simulation. The water structure and water-polymer interaction was investigated from the radial distribution function and the viewpoint of the hydrogen-bonding system. It is found that the hydrogen bonds between polymer and water strongly depress the diffusion of water molecules and enhance the structure of water in the system. The greater the network mesh size of the polymer, the weaker the structure of the water. The decreasing of the density of hydrogen bonds between polymer and water is the major factor that leads to the weakening of water structure.     

Structural studies on the hydration of L-glutamic acid in solution

A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.     

Proteins, lipids, and water in the gas phase

Evidence from mass‐spectrometry experiments and molecular dynamics simulations suggests that it is possible to transfer proteins, or in general biomolecular aggregates, from solution to the gas‐phase without grave impact on the structure. If correct, this allows interpretation of such experiments as a probe of physiological behavior. Here, we survey recent experimental results from mass spectrometry and ion‐mobility spectroscopy and combine this with observations based on molecular dynamics simulation, in order to give a comprehensive overview of the state of the art in gas‐phase studies. We introduce a new concept in protein structure analysis by determining the fraction of the theoretical possible numbers of hydrogen bonds that are formed in solution and in the gas‐phase. In solution on average 43% of the hydrogen bonds is realized, while in vacuo this fraction increases to 56%. The hydrogen bonds stabilizing the secondary structure (α‐helices, β‐sheets) are maintained to a large degree, with additional hydrogen bonds occurring when side chains make new hydrogen bonds to rest of the protein rather than to solvent. This indicates that proteins that are transported to the gas phase in a native‐like manner in many cases will be kinetically trapped in near‐physiological structures. Simulation results for lipid‐ and detergent‐aggregates and lipid‐coated (membrane) proteins in the gas phase are discussed, which in general point to the conclusion that encapsulating proteins in “something” aids in the conservation of native‐like structure. Isolated solvated micelles of cetyl‐tetraammonium bromide quickly turn into reverse micelles whereas dodecyl phosphocholine micelles undergo much slower conversions, and do not quite reach a reverse micelle conformation within 100 ns.