Substructure isomorphism matrix

A substructure isomorphism matrix n x p contains binary elements describing which of the given p query structures (substructures) are part of the given n target structures (molecular structures). Such a matrix can be used to investigate the diversity of the target structures and allows the characterization and comparison of structural libraries. A quadratic substructure isomorphism matrix n x n is obtained if the same structures are used as molecular structures and as substructures; this matrix contains full information about the topological hierarchy of the n structures. A hierarchical arrangement of chemical structures is useful for the evaluation of results obtained from searches in structure databases.     

Identify crystal structures by a new paradigm based on graph theory for building materials big data

Material identification technique is crucial to the development of structure chemistry and materials genome project. Current methods are promising candidates to identify structures effectively, but have limited ability to deal with all structures accurately and automatically in the big materials database because different material resources and various measurement errors lead to variation of bond length and bond angle. To address this issue, we propose a new paradigm based on graph theory(GTscheme) to improve the efficiency and accuracy of material identification, which focuses on processing the "topological relationship" rather than the value of bond length and bond angle among different structures. By using this method, automatic deduplication for big materials database is achieved for the first time, which identifies 626,772 unique structures from 865,458 original structures.Moreover, the graph theory scheme has been modified to solve some advanced problems such as identifying highly distorted structures, distinguishing structures with strong similarity and classifying complex crystal structures in materials big data.     

Incremental solvation of nonionized and zwitterionic glycine

Microsolvation and combined microsolvation-continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3-5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7-9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine.     

Three-dimensional assembly of flower-like Au structures: the synergistic effect of macroporous structures and surface nanoarchitectures on electrocatalysis and electroanalysis

We present the fabrication of a three-dimensional (3D) assembly of flower-like Au structures via the combination of 3D macroporous Au-coated microspheres and surface nanoarchitectures using electrodeposition of nanoplate Au structures. The 3D flower-like Au structures exhibit synergistically enhanced electrocatalytic activities regarding glucose oxidation and oxygen reduction compared to those of the individual 3D macroporous and nanoplate Au structures. The 3D flower-like Au structures can also be utilized as electroanalytical platforms retaining the combined advantages of both of the 3D macroporous and nanoplate Au structures.     

Coding and ordering Kekulé structures

The concept of numerical Kekulé structures is used for coding and ordering geometrical (standard) Kekulé structures of several classes of polycyclic conjugated molecules: catacondensed, pericondensed, and fully arenoid benzenoid hydrocarbons, thioarenoids, and [N]phenylenes. It is pointed out that the numerical Kekulé structures can be obtained for any class of polycyclic conjugated systems that possesses standard Kekulé structures. The reconstruction of standard Kekulé structures from the numerical ones is straightforward for catacondensed systems, but this is not so for pericondensed benzenoid hydrocarbons. In this latter case, one needs to use two codes to recover the geometrical Kekulé structures: the Wiswesser code for the benzenoid and the numerical code for its Kekulé structure. There is an additional problem with pericondensed benzenoid hydrocarbons; there appear numerical Kekulé structures that correspond to two (or more) geometrical Kekulé structures. However, this problem can also be resolved.     

柔软的球状和长方体状氧化硅中空结构的制备研究

采用自组装形成的芘纳米结构作为模板,成功地制备了柔软的球状和长方体状氧化硅中空结构.当不同量的芘在十六烷基三甲基溴化铵(CTAB)溶液中自组装时,产生的自组装结构展现出明显的从球状到长方体状的形貌变化.这些结构被用作氧化硅前驱体溶胶-凝胶反应的模板,获得了球状和长方体状氧化硅/芘复合结构.通过乙醇除去模板后,生成了柔软的球状(直径约为400nm)和长方体状(长为0.5—2.5μm)的氧化硅中空结构.这些结果展现了采用有机纳米结构作为模板来合成无机中空结构的优势:合成简便、结构多样以及结构形貌的灵活可控.     

隐藏高分子界面及生物界面分子结构的和频振动光谱研究

界面的分子结构决定界面的性质.为了以优化界面的结构来改进材料的性质,原位实时地研究界面的分子结构是很重要的.近年来和频振动光谱已发展成为一个很有效及独特的手段来研究隐藏界面的分子结构,例如液/液界面、固/液界面及固/固界面等.这篇综述讨论了和频振动光谱在研究高分子界面及生物界面等复杂界面的分子结构上的应用.具体说来,本文论述了高分子表面在水里的分子结构变化,高分子及模型粘合促进剂硅烷在界面相互作用的分子机理和隐藏的高分子/高分子及高分子/金属界面的结构.另外,此文还将介绍不同二级结构的多肽及几个有代表性的蛋白分子在界面的结构.界面在诸如化学、生物、物理、材料科学及工程和纳米技术等许多领域都很重要.发展一个独特的能原位研究隐藏界面的分子结构的技术会有力地促进这些领域的研究及跨学科研究的发展.     

Generation of Kekulé valence structures and the corresponding valence bond wave function

A new scheme, called "list of nonredundant bonds", is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p-orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time.     

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures

The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model’s quality and investigate protein-induced strain.     

Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures

Incorporating receptor flexibility is considered crucial for improvement of docking-based virtual screening. With an abundance of crystallographic structures freely available, docking with multiple crystal structures is believed to be a practical approach to cope with protein flexibility. Here we describe a successful application of the docking of multiple structures to discover novel and potent Chk1 inhibitors. Forty-six Chk1 structures were first compared in single structure docking by predicting the binding mode and recovering known ligands. Combinations of different protein structures were then compared by recovery of known ligands and an optimal ensemble of Chk1 structures were selected. The chosen structures were used in the virtual screening of over 60?000 diverse compounds for Chk1 inhibitors. Six novel compounds ranked at the top of the hits list were tested experimentally, and two of these compounds inhibited Chk1 activity-the best with an IC(50) value of 9.6 μM. Further study indicated that achieving a better enrichment and identifying more diverse compounds was more likely using multiple structures than using only a single structure even when protein structures were randomly selected. Taking into account conformational energy difference did not help to improve enrichment in the top ranked list.     

Calorimetric study of the native and postdenatured structures in starches with different degree of hydration

DSC studies of melting process of annealed native structures and postdenatured ones in low-amylose starches with different degrees of hydration were carried out. The starch recrystallization at different thermal treatments of the samples was studied both after the complete and partial destroy of native structures. It has been shown that native structures as well as postdenatured ones possess the ability to perfection, which is most clearly seen at the annealing at temperatures inside their melting ranges. The results obtained demonstrate that at the same duration of annealing the process of crystal perfection for secondary starch structures proceed more intensively compared to the native ones. The presence of the remained native structures in partial melt in contrast to the remained gel ones restricts the ability of the recrystallized structures to perfection.     

Studies in hydrogen bonding: simulation of the crystalline solids of ice, ammonia, and ammonia hydrate

The crystal structures of ice, ammonia and ammonia hydrate have been simulated with rigid molecules using the interatomic potential function EPEN/2 and the computer program WMIN. Structural parameters were adjusted to give structures with minimum energy. The hydrogen bonding in the simulated structures is compared with that in the experimental structures.     

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.     

Templated growth of hybrid structures at the peptide-peptide interface

This study describes the use of peptide vesicular platforms for the templated growth of fibrillar structures to craft hybrids that retain the gross morphological features of two discreet self-assembled peptides. A synthetic triskelion peptide, which results in the rapid emergence of self-assembled spherical structures, was employed as a template. Addition of either one of two different peptides, both of which form long filamentous structures when co-incubated with the triskelion solution, affords hybrids that retain the gross morphology of both the spherical and filamentous structures. It is surmised that this process is aided by hydrogen bonding and the interdigitation of aromatic residues, which leads to the growth of hybrid structures. We believe that observations concerning the surface-assisted growth of peptide fibrils and tubular structures from vesicular platforms may have ramifications for the design and development of peptide-based hybrid materials with controlled hierarchical structures.     

Phase segregation of a symmetric diblock copolymer in constrained space with a square-pillar array

In this study, we apply a self-consistent field theory of polymers to study the structures of a symmetric diblock copolymer in parallel substrates filled with square-pillar arrays in which the substrates and pillars exhibit a weak preference for one block of the copolymer. Three classes of structures, i.e., lamellae, perpendicular cylinders, and bicontinuous structures, are achieved by varying the polymer film thickness, the pillar pitch (the distance between two centers of the nearest neighboring pillars), the gap and rotation of the pillars. Because of the confinement along horizontal directions imposed by the pillar array, eight novel types of perpendicular lamellar structures and eight novel types of cylindrical structures with various shapes and distributions occur. In the hybridization states of the parallel and perpendicular lamellar structures, several novel bicontinuous structures such as the double-cylinder network, pseudo-lamellae, and perforated lamellar structure are also found. By comparing the free energies of the various possible structures, the antisymmetric parallel lamellae are observed to be stable with the larger pillar gap at a certain film thickness. The structural transformations between the alternating cylindrical structures (alternating cross-shaped, square-shaped, and octagonal perpendicular cylinders) and parallel lamellae with increasing film thickness or pillar gap are well explained by the modified strong separation theory. Our results indicate that array confinement can be an effective method to prepare novel polymeric nanopattern structures.     

Engineering nonspherical hollow structures with complex interiors by template-engaged redox etching

Despite the significant advancement in making hollow structures, one unsolved challenge in the field is how to engineer hollow structures with specific shapes, tunable compositions, and desirable interior structures. In particular, top-down engineering the interiors inside preformed hollow structures is still a daunting task. In this work, we demonstrate a facile approach for the preparation of a variety of uniform hollow structures, including Cu(2)O@Fe(OH)(x) nanorattles and Fe(OH)(x) cages with various shapes and dimensions by template-engaged redox etching of shape-controlled Cu(2)O crystals. The composition can be readily modulated at different structural levels to generate other interesting structures such as Cu(2)O@Fe(2)O(3) and Cu@Fe(3)O(4) rattles, as well as Fe(2)O(3) and Fe(3)O(4) cages. More remarkably, this strategy enables top-down engineering the interiors of hollow structures as demonstrated by the fabrication of double-walled nanorattles and nanoboxes, and even box-in-box structures. In addition, this approach is also applied to form Au and MnO(x) based hollow structures.     

Accelerating the detection of unfeasible hypothetical zeolites via symmetric local interatomic distance criteria

In silico prediction of potential synthetic targets is the prerequisite for function-led discovery of new zeolites. Millions of hypothetical zeolitic structures have been predicted via various computational methods, but most of them are experimentally inaccessible under conventional synthetic conditions. Screening out unfeasible structures is crucial for the selection of synthetic targets with desired functions. The local interatomic distance (LID) criteria are a set of structure rules strictly obeyed by all existing zeolite framework types. Using these criteria, many unfeasible hypothetical structures have been detected. However, to calculate their LIDs, all hypothetical structures need to be fully optimized without symmetry constraints. When evaluating a large number of hypothetical structures, such calculations may become too computationally expensive due to the forbiddingly high degree of freedom. Here, we propose calculating LIDs among structures optimized with symmetry constraints and using them as new structure evaluation criteria, i.e., the LID_sym criteria, to screen out unfeasible hypothetical structures. We find that the LID_sym criteria can detect unfeasible structures as many as the original non-symmetric LID criteria do, yet require at least one order of magnitude less computation at the initial geometry optimization stage.     

Global reaction route mapping on potential energy surfaces of formaldehyde, formic acid, and their metal-substituted analogues

Global reaction route mapping of equilibrium structures, transition structures, and their connections on potential energy surface (PES) has been done for MCHO (M = H, Li, Na, Al, Cu) and HCO2M (M = H, Li). A one-after-another technique based on the scaled hypersphere search method has been successfully applied to exploring unknown chemical structures, transition structures, and reaction pathways for organometallic systems. Upon metal substitution, considerable changes of stable structures, reaction pathways, and relative heights of transition structures have been discovered, though some features are similar among the analogues. Al and Cu atoms were found to behave as very strong scissors to cut the CO double bond in MCHO. Energy profiles of the CO insertion into Li-H and Li-CH3 bonds were found to be very similar, especially around the structures where the Li atom is not directly connected with the methyl group, which indicates little effects of alkyl substitution on the reaction route topology.     

Temperature and Composition Dependent Structural Evolution: Thermodynamics of CunAg135−n (n = 0–135) Nanoalloys during Cooling

Molecular dynamics simulations are performed to investigate the changes of packing structures, and thermodynamic quantities including internal energy, entropy, and free energy are used to determine temperature regime and transition time of atomic packing structures. The simulation results show different packing structures as the component composition changes, and there are different packing patterns during cooling. For these Cu-Ag alloy clusters containing only a small number of atoms of Cu, they present FCC packing structures in different parts at high temperatures, and then there are transformations to icosahedral structures. With the increase in content of Cu atoms, there is a transition mechanism from molten state to icosahedron. When the content of Cu atoms is appropriate, core-shell structures can be formed at room temperature.     

Chemical evaluation of hypothetical uninodal zeolites

Optimized structural parameters, framework energies relative to alpha-quartz, and volumes accessible to sorption have been calculated for the systematically enumerated hypothetical uninodal zeolitic structures (structures in which all tetrahedral sites are equivalent). The structures were treated as silica polymorphs, and their energies were minimized using the GULP program with the Sanders-Catlow silica potential. Results are given for 164 structures, which include all 21 known uninodal zeolites, two known minerals (tridymite and cristobalite), and 78 unknown zeolite topologies. Twenty-three hypothetical structures were identified as chemically feasible. Complete structural information is provided, and several structures are discussed in detail. The results will assist in the design of new synthetic routes and in the identification of newly synthesized materials.