Interfacial characteristics of heterogeneous layers of linear polyvinylamine and branched polyethyleneimine or polyethyleneimine grafted with C12-C22 alkyl chains

We investigated the characteristics of heterogeneous layers composed of linear hydrolyzed polyvinylamine and branched polyethyleneimine adsorbed at silica/water interfaces. The studies also included heterogeneous layers where branched polyethyleneimine was replaced by polyethyleneimine modified by grafting with C12-C22 alkyl chains. Surface area exclusion chromatography was used to determine the interfacial relaxation and surface affinity of the polymer molecules within homogeneous layers. The relaxation of bare and grafted polyethyleneimine was found to be small and of equal extent but to develop at different rates. Comparatively, the relaxation of hydrolyzed polyvinylamine was faster and of greater extent. Within heterogeneous layers composed of polyvinylamine and bare or grafted polyethyleneimine, the relaxation of the different molecules was strongly increased as compared to that prevailing in homogeneous layers. The chromatographic method was then used to determine the mode of layer establishment. The polymer coating profiles on successive glass fiber filters were found to depend on the sequence of injection of the two polymers, due to the interfacial stability or instability of the initially established layer. It was shown that a previously established extremely thin layer of bare or grafted polyethyleneimine molecules strongly modified the adsorption profile of subsequently adsorbed polyvinylamine molecules.     

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode‐mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc.     

Relaxation phenomena of hydrolyzed polyvinylamine molecules adsorbed at the silica/water interface II. Saturated heterogeneous polymer layers

Surface area exclusion chromatography (SAEC) was employed to determine the individual relaxation of polymer molecules within a saturated heterogeneous layer composed of two polymers of different molecular characteristics. The investigations focused on three systems differing in molecular weight and/or hydrolysis grade. The molecular relaxation process was determined to be different within the heterogeneous layer when compared with the behavior of the same polymer in the homogeneous layer. The modifications in the relaxation process of a given polymer were imposed by the interfacial characteristics of the second polymer. Finally, in heterogeneous layers, the relative variation of the interfacial area of the two polymers is expressed in a single relationship.     

Framework materials assembled from magnesium carboxylate building units

Four coordination polymers containing magnesium metal nodes and di- or tricarboxylic acid organic connectors have been synthesised and structurally characterised with the aid of single crystal X-ray diffraction. Mg3(bdc)3(DMA)4 (1) and Mg3(bdc)3(EtOH)2 (2) were prepared from the 1 : 1 reaction of 1,4-benzenedicarboxylic acid (H(2)bdc) with Mg(NO3)2.6H2O in dimethylacetamide (DMA) or EtOH respectively. Both 1 and 2 contain tri-metallic magnesium carboxylate units which act as six-coordinate nodes for network construction. These tri-magnesium nodes are joined by the bdc ligands in 1 to give a 2D layered structure with coordinated DMA solvent molecules between the layers, whereas in 2 they stack end-on to form a novel 3D network containing 1D Mg carboxylate chains. Both 1 and 2 are moderately hygroscopic, and powder X-ray diffraction and thermogravimetric analysis studies show them to be interconvertible with Mg(bdc) and the hydrated complex Mg(bdc)(H2O)2 via a series of solid-state reactions. Reaction of magnesium nitrate with 4,4'-biphenyldicarboxylic acid (H(2)bpdc) in DMA gives Mg3(bpdc)3(DMA)4 (3), which in contrast to 2 forms a 'squashed' 3D cubic network as a result of the increased distance between the trinuclear nodes necessitated by the longer bpdc ligands. Reaction of magnesium nitrate with the triangular organic building block 1,3,5-tricarboxylic acid (H(3)btc) in DMA gives crystals of Mg(H(1.5)btc)2/3(btc)1/3(DMA)2.(DMA)1/3 (4). Compound 4 contains mono-metallic metal nodes which assemble with the btc ligands to give 2D 6(3) tessellated layers with Mg-coordinated DMA molecules lying perpendicular to the layers. Some free DMA is also present in 4, sited in small pores between the layers.     

Molecular dynamic simulation methods for anisotropic liquids

Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well.     

Simulated molecular evolution in a full combinatorial library

BACKGROUND: The Darwinian concept of 'survival of the fittest' has inspired the development of evolutionary optimization methods to find molecules with desired properties in iterative feedback cycles of synthesis and testing. These methods have recently been applied to the computer-guided heuristic selection of molecules that bind with high affinity to a given biological target. We describe the optimization behavior and performance of genetic algorithms (GAs) that select molecules from a combinatorial library of potential thrombin inhibitors in 'artificial molecular evolution' experiments, on the basis of biological screening results. RESULTS: A full combinatorial library of 15,360 members structurally biased towards the serine protease thrombin was synthesized, and all were tested for their ability to inhibit the protease activity of thrombin. Using the resulting large structure-activity landscape, we simulated the evolutionary selection of potent thrombin inhibitors from this library using GAs. Optimal parameter sets were found (encoding strategy, population size, mutation and cross-over rate) for this artificial molecular evolution. CONCLUSIONS: A GA-based evolutionary selection is a valuable combinatorial optimization strategy to discover compounds with desired properties without needing to synthesize and test all possible combinations (i.e. all molecules). GAs are especially powerful when dealing with very large combinatorial libraries for which synthesis and screening of all members is not possible and/or when only a small number of compounds compared with the library size can be synthesized or tested. The optimization gradient or 'learning' per individual increases when using smaller population sizes and decreases for higher mutation rates.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Scaffold hopping using clique detection applied to reduced graphs

Similarity-based methods for virtual screening are widely used. However, conventional searching using 2D chemical fingerprints or 2D graphs may retrieve only compounds which are structurally very similar to the original target molecule. Of particular current interest then is scaffold hopping, that is, the ability to identify molecules that belong to different chemical series but which could form the same interactions with a receptor. Reduced graphs provide summary representations of chemical structures and, therefore, offer the potential to retrieve compounds that are similar in terms of their gross features rather than at the atom-bond level. Using only a fingerprint representation of such graphs, we have previously shown that actives retrieved were more diverse than those found using Daylight fingerprints. Maximum common substructures give an intuitively reasonable view of the similarity between two molecules. However, their calculation using graph-matching techniques is too time-consuming for use in practical similarity searching in larger data sets. In this work, we exploit the low cardinality of the reduced graph in graph-based similarity searching. We reinterpret the reduced graph as a fully connected graph using the bond-distance information of the original graph. We describe searches, using both the maximum common induced subgraph and maximum common edge subgraph formulations, on the fully connected reduced graphs and compare the results with those obtained using both conventional chemical and reduced graph fingerprints. We show that graph matching using fully connected reduced graphs is an effective retrieval method and that the actives retrieved are likely to be topologically different from those retrieved using conventional 2D methods.     

Application of belief theory to similarity data fusion for use in analog searching and lead hopping

A wide variety of computational algorithms have been developed that strive to capture the chemical similarity between two compounds for use in virtual screening and lead discovery. One limitation of such approaches is that, while a returned similarity value reflects the perceived degree of relatedness between any two compounds, there is no direct correlation between this value and the expectation or confidence that any two molecules will in fact be equally active. A lack of a common framework for interpretation of similarity measures also confounds the reliable fusion of information from different algorithms. Here, we present a probabilistic framework for interpreting similarity measures that directly correlates the similarity value to a quantitative expectation that two molecules will in fact be equipotent. The approach is based on extensive benchmarking of 10 different similarity methods (MACCS keys, Daylight fingerprints, maximum common subgraphs, rapid overlay of chemical structures (ROCS) shape similarity, and six connectivity-based fingerprints) against a database of more than 150,000 compounds with activity data against 23 protein targets. Given this unified and probabilistic framework for interpreting chemical similarity, principles derived from decision theory can then be applied to combine the evidence from different similarity measures in such a way that both capitalizes on the strengths of the individual approaches and maintains a quantitative estimate of the likelihood that any two molecules will exhibit similar biological activity.     

Symmetries and fuzzy symmetries of graphene molecules

In this paper, we will investigate the fuzzy layer group symmetries of two-dimensional (2D) periodic molecules. Here, we select several graphene molecules as typical examples to discuss. For these two-dimensional graphene molecules, their MO energies, symmetries and fuzzy symmetries are preliminarily studied. In addition, we especially make a detailed comparison between the zigzag and armchair graphene molecules. These studies will develop a theoretical framework that will help us to investigate the fuzzy symmetries of various layer group molecules as well as molecules with 3D periodic structure.     

Autonomous Supramolecular Interface Self-Healing Monitored by Restoration of UV/Vis Absorption Spectra of Self-Assembled Thiazole Layers

Longevity of complex organic devices critically depends on the supramolecular integrity of the constituting layers and interfaces. Because the latter are soft matter, they can structurally respond to perturbation of their supramolecular structure by relaxing back to a thermodynamically favorable state. To use this response for self-healing of optoelectronically active layers and particularly interfaces, the degraded dyes in these layers need to be exchanged with non-degraded ones. Here, we present a dye layer interfaced between a solid surface and a dye reservoir that autonomously self-heals after photo-degradation of single molecules to restore its optical function. Surface sensitive in situ photothermal deflection spectroscopy reveals that this supramolecular self-healing approach critically depends on the thermodynamic stability of the layer, the chemical change of the dye upon degradation, and the medium dissolving the degraded dye and providing the reservoir dyes. Hence, the interplay of these parameters is key to successfully using this supramolecular self-healing approach to thin layers and interfaces in organic device for increased sustainability of organic optoelectronics and related fields.     

Crystal growth of para-sexiphenyl on clean and oxygen reconstructed Cu(110) surfaces

The formation of crystalline para-sexiphenyl (6P) films on Cu(110) and Cu(110)-(2 × 1)O (Cu-O) has been studied by low energy electron diffraction, X-ray absorption spectroscopy and both in situ and ex situ X-ray diffraction methods to elucidate the transition from the initial monolayers to crystalline thin films. It is found that, for Cu-O, a single and, for Cu(110), a double wetting layer is formed which then acts as a template for the subsequent 3D crystal growth. For both substrates the orientation of the long molecular axes of the 6P molecules in the first layers is conserved for the molecules in the bulk crystals growing on them. The main difference between both systems is that on Cu-O the first monolayer assembles in a form close to that of a 6P bulk plane which can be easily continued by crystallites grown upon them, while on the Cu(110) surface the 6P mono- and bi-layers differ substantially from the bulk structure. The bi-layer forms a complex periodically striped phase. Thin 6P films grow with the 6P(203) crystal plane parallel to the Cu-O substrate surface. For this orientation, the 6P molecules are stacked in layers and the molecules demonstrate only one tilt of the mean molecular plane with respect to the sample surface. On clean Cu(110), a more complex 6P(629) plane is parallel to the substrate surface and this orientation is likely a consequence of the super-molecular long-range periodicity of the second molecular layer striped phase.     

A New Series of Charge-assisted Hydrogen-bonded Host Frameworks Based on [Co（en）_3]~（3＋）and Dicarboxylates

A new series of metal complex carboxylates(MCC)made of [Co(en)3]3+(MC)and either 2,6-naphthalenedicarboxylic(NDC)or 4,4-biphenyldicarboxylic(BPDC)were synthesized and structurally characterized.The four new compounds have a general formula(MC)2(C)3·n(guest)with the guests of dimethylformamide(DMF)and dimethyl sulfoxide(DMSO)and water.All the structures represent a pillared-layer type,where the layer consists of MC cations,carboxylate anions or water molecules via a large number of hydrogen bonds.The layers are pillared by the organic residues of NDC or BPDC,resulting in the inclusion cavities where the guest molecules reside.Although their topological structures are similar,they crystallize in different crystal structures due to the rearrangement of pillars and hydrogen-bonded layers.     

The nature of cationic adsorption sites in alkaline zeolites--single, dual and multiple cation sites

Gas adsorption on zeolites constitutes the base of many technological applications of these versatile porous materials. Quite often, especially when dealing with small molecules, individual extra-framework (exchangeable) cations are considered to be the adsorption site on which molecules coming from a gas phase form the corresponding adsorption complex. Nonetheless, while that can be the case in some instances, recent research work that combines variable temperature infrared spectroscopy with periodic DFT calculations showed that some types of adsorption sites involve two or more cations, which constitute dual and multiple cation sites, respectively. Adsorption complexes formed on these cationic adsorption sites differ in both structure and stability from those formed on a single cation alone. Examples concerning CO, CO(2) and H(2) adsorption on alkali and alkaline-earth metal exchanged zeolites are reviewed, with the double purpose of clarifying concepts and highlighting their relevance to practical use of zeolites in such fields as gas separation and purification, gas storage and heterogeneous catalysis.     

PET表面的碳氟等离子体处理改性层组分的变角XPS分析

采用CH₄/CF₄混合气体等离子体来处理PET表面.利用变角XPS研究改性后PET的表面改性层的组分随取样深度的变化.结果表明,碳氟混合气体等离子体在PET表面形成交联网络结构的改性层,改性层的化学组成随深度的变化不大;纯CF₄等离子体的改性层的化学组成不均匀,含氟基团主要分布在外面.不同混合气体等离子体在PET表面形成改性层的结构决定于CH₄的添加量.     

Molecular dynamics simulation of surface segregation in a (110) B2-NiAl thin film

Surface segregation in (110) B2-NiAl film approximately 3 nm thick is investigated by using molecular dynamics simulation with a reliable embedded-atom potential. The simulation is performed for the stoichiometric composition at a temperature of 1500 K, just below the melting temperature of the film model. It is found that the (110) surface is structurally stable but develops adatoms, vacancies and antisites. The coverage of an adatom layer is estimated to be ～0.07 ML (monatomic layers) and it contains on average ～95% of Al atoms. The top (surface) and second (subsurface) layers of the (110) surface is the most enriched in Ni relative to the bulk composition. These layers contain on average ～51% of Ni atoms. The Ni fraction in the third and forth layers of the film is estimated as ～50.5%. The deeper layers have essentially the bulk composition. Vacancies in the film model are found only on the Ni sublattice. The vacancy concentration on the Ni sublattice in the top layer is ～7.5%. The second layer almost does not contain vacancies. The next layers have essentially the constant bulk vacancy composition which can be estimated as ～1.3-1.4%.