The effect of proton disorder on the structure of ice-Ih: a theoretical study

A precise and accurate measurement of the crystal structure of ice-Ih is hindered by its disordered H-bond network. In this work, we carried out first-principle calculations to study the effects of H-bond topology on the structure of ice-Ih with emphasis on the molecular geometry of water and the distortion in oxygen lattice. An analytic algorithm based on group and graph theory is employed to enumerate all possible configurations in a given unit cell and to select a set of structures for detailed examinations. In total we have studied more than 60 ice-Ih structures in a hexagonal unit cell of 48 water molecules by quantum-chemical methods and found a significant amount of static distortion in the oxygen positions from their crystallographic positions which is in good agreements with highly significant higher-order terms obtained from both x-ray and neutron-diffraction data. Much debated structural information such as H-O-H angle and O-H bond length is found to be 106.34+/-0.36 degrees and 0.9997+/-0.0008 A, compared to experimental value of 106.6+/-1.5 degrees and 0.986+/-0.005 A. Detailed benchmarking calculations were carried out to gauge the influence of using different exchange and correlation functionals, pseudopotentials, and unit-cell sizes. Our results have proven that first-principle methods are useful complementary tools to experiments, especially for cases in which experimental accuracy is limited by intrinsic orientational disorder.     

Self-organisation in the assembly of gels from mixtures of different dendritic peptide building blocks

This paper investigates dendritic peptides capable of assembling into nanostructured gels, and explores the effect on self-assembly of mixing different molecular building blocks. Thermal measurements, small angle X-ray scattering (SAXS) and circular dichroism (CD) spectroscopy are used to probe these materials on macroscopic, nanoscopic and molecular length scales. The results from these investigations demonstrate that in this case, systems with different "size" and "chirality" factors can self-organise, whilst systems with different "shape" factors cannot. The "size" and "chirality" factors are directly connected with the molecular information programmed into the dendritic peptides, whilst the shape factor depends on the group linking these peptides together--this is consistent with molecular recognition hydrogen bond pathways between the peptidic building blocks controlling the ability of these systems to self-recognise. These results demonstrate that mixtures of relatively complex peptides, with only subtle differences on the molecular scale, can self-organise into nanoscale structures, an important step in the spontaneous assembly of ordered systems from complex mixtures.     

Photocurable glycidoxypropyltrimethoxysilane based sol-gel hybrid materials

Hybrid sol-gel materials are promising candidates for electro/optical applications, combining the most important glass-like and polymer-like properties. Hybrid patternable materials produced by photopolymerisation processes have been mainly developed on 3-methacrloxypropyltrimethoxysilane based systems in which the polymerisable organic function is the CC bond of the methacrylic group. A new photosensitive hybrid material is described here, based on 3-glycidoxypropyltrimethoxysilane (GPTMS) and on the cationic photopolymerisation of the epoxide groups, which lead to the formation of a PEO organic interpenetrating network.     

Identifying promising metal–organic frameworks for heterogeneous catalysis via high-throughput periodic density functional theory

Metal–organic frameworks (MOFs) are a class of nanoporous materials with highly tunable structures in terms of both chemical composition and topology. Due to their tunable nature, high-throughput computational screening is a particularly appealing method to reduce the time-to-discovery of MOFs with desirable physical and chemical properties. In this work, a fully automated, high-throughput periodic density functional theory (DFT) workflow for screening promising MOF candidates was developed and benchmarked, with a specific focus on applications in catalysis. As a proof-of-concept, we use the high-throughput workflow to screen MOFs containing open metal sites (OMSs) from the Computation-Ready, Experimental MOF database for the oxidative C—H bond activation of methane. The results from the screening process suggest that, despite the strong C—H bond strength of methane, the main challenge from a screening standpoint is the identification of MOFs with OMSs that can be readily oxidized at moderate reaction conditions. © 2019 Wiley Periodicals, Inc.     

Density functional theory for semiflexible and cyclic polyatomic fluids

The effects of bond angle and chain stiffness on the structures of semiflexible polyatomic fluids are investigated by incorporating the bending potential into a density functional theory [Y. X. Yu and J. Z. Wu, J. Chem. Phys. 117, 2368 (2002)] that combines a modified fundamental measure theory for the excluded-volume effects and the first-order thermodynamics perturbation theory for the chain connectivity. The refined density functional theory faithfully reproduces the density profiles and conformational properties of a variety of triatomic fluids near a hard wall in which extensive Monte Carlo simulation data are available. In particular, the theory is able to capture the structures of rigid cyclic trimers where all segments are identical. The variation of local density profiles with respect to the chain length of confined polyatomic fluids is also explored. For quadratomic fluids confined in slit pores, the density profile of the middle segments exhibits novel double peaks that are absent in a fully flexible chain model. In addition, the density functional theory is applied to predicting the conformational properties and adsorption behavior of heterogeneous triatomic fluids of type "ABB" mimicking surfactant molecules. The competition between surface adsorption and self-association of trimers consisting of surface active and self-binding "A" segments and neutral "B" segment is explored.     

Polycyclic aromatic hydrocarbons with five-membered rings: Modeling of experimental X-ray and neutron-diffraction structures

Several of the readily available theoretical programs are evaluated as tools for modeling the structures of polycyclic aromatic hydrocarbons with five-membered rings (CPAHs). The experimentally determined bond lengths and angles are compared to calculated values. Experimental bond lengths are also compared to Pauling and Huckel molecular orbital (HMO) bond orders. Previously published experimental X-ray and neutron-diffraction structures of acenaphthene, acenaphthylene, fluoranthene, cyclopent[o,p,q,r]benz[c]phenanthrene, and corannulene are modeled by the programs MMX, AM1, MNDO, and PM3, and previously reported STO-3G and 6-31G * data are also evaluated. In general, the error differences between the experimental and calculated results for all of the semiempirical programs were small. However, PM3 performed slightly better than AM1 and MMX, while MNDO generated structures which exhibited the largest deviation from experiment. Although the standard deviations for all programs are shown to be of comparable magnitude, a particular bond length or bond angle in any given theoretical calculation can exhibit significant error from the experimental data. The scatter in the bond order data computed from Huckel molecular orbital theory and valence bond theory is contrary to results obtained with alternant systems. It appears that these approaches are less successful at modeling accurately the nonalternant hydrocarbon systems described in this paper.     

Database mining using soft computing techniques. An integrated neural network-fuzzy logic-genetic algorithm approach

Two different soft computing (SC) techniques (a competitive learning neural network and an integrated neural network-fuzzy logic-genetic algorithm approach) are employed in the analysis of a database subset obtained from the Cambridge Structural Database. The chemical problem chosen for study is relevant to the relationship between various metric parameters in transition metal imido (LnMdNZ, Z = carbon-based substituent) complexes and the chemical consequences of such relationships. The SC techniques confirmed and quantified the suspected relationship between the metal-nitrogen bond length and the metal-nitrogen-substituent bond angle for transition metal imidos: increased metal-nitrogen-carbon angles correlate with shortened metal-nitrogen distances. The mining effort also yielded an unexpected correlation between the NC distance and the MNC angle-shorter NC correlate with larger MNC. A fuzzy inference system is used to construct an MNred-NC-MNC hypersurface. This hypersurface suggests a complicated interdependence among NC, MNred, and the angle subtended by these two bonds. Also, major portions of the hypersurface are very flat, in regions where MNC is approaching linearity. The relationships are also seen to be influenced by whether the imido substituent is an alkyl or aryl group. Computationally, the present results are of particular interest in two respects. First, SC classification was able to isolate an "outlier" cluster. Identification of outliers is important as they may correspond to unreported experimental errors in the database or novel chemical entities, both of which warrant further investigation. Second, the SC database mining not only confirmed and quantified a suspected relationship (MNred versus MNC) within the data but also yielded a trend that was not suspected (NC versus MNC).     

非晶硅短程序与电子结构关系的量子化学研究

本支通过对Si_(29)无规网络原子簇模型的CNDO计算,探讨了非晶硅(a-Si)结构短程序对其电子态密度(DOS)分布的影响。结果表明,在与实验原子径向分布函数(RDF)基本相同的条件下,a-Si模型中的键角和二面角是影响电子态密度分布的主要参数。     

Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs

This paper reports a method for the identification of those molecules in a database of rigid 3D structures with molecular electrostatic potential (MEP) grids that are most similar to that of a user-defined target molecule. The most important features of an MEP grid are encoded in field-graphs, and a target molecule is matched against a database molecule by a comparison of the corresponding field-graphs. The matching is effected using a maximal common subgraph isomorphism algorithm, which provides an alignment of the target molecule's field- graph with those of each of the database molecules in turn. These alignments are used in the second stage of the search algorithm to calculate the intermolecular MEP similarities. Several different ways of generating field-graphs are evaluated, in terms of the effectiveness of the resulting similarity measures and of the associated computational costs. The most appropriate procedure has been implemented in an operational system that searches a corporate database, containing ca. 173,000 3D structures.     

Conformational Aspects and Intramolecular Phase Separation of Alternating Copolymacromonomers: A Computer Simulation Study

Summary: Using the bond fluctuation model (BFM), simulations have been performed on molecular bottle brushes with two chemically different types of side chains. In the first part of this work, rigidity of the backbone is imposed. The influence of solvent quality and side chain length on the intramolecular phase separation of side chain material, leading to Janus cylinders, has been investigated and compared to theoretical predictions. In the second part of this work, the restriction of rigidity for the backbone is relaxed. In a poor solvent, the side chain material collapses into a globular state. Several globules containing each one type of side chain material are connected together by backbone material. When imposing different solvent conditions for both types of side chains, a bending of the backbone is found as predicted by theory and observed in very recent experiments.

Comparison between typical snapshots in θ solvent. The side chain length is 25 beads. Dark and light coloured side chains repel each other.     

Polysulfide anions II: structure and vibrational spectra of the S4(2-) and S5(2-) anions. Influence of the cations on bond length, valence, and torsion angle

The influence of the cations on bond length, valence, and torsion angle of S4(2-) and S5(2-) anions was examined in a series of solid alkali tetra- and pentasulfides by relating their Raman spectra to their known X-ray structures through a force-field analysis. The IR and Raman spectra of BaS4.H2O and the Raman spectra of (NH4)2S4.nNH3, gamma-Na2S4, and delta-Na2S5 are presented. The similarity of spectra of gamma-Na2S4 with those of BaS4.H2O suggests similar structures of the S4(2-) anions in these two compounds with a torsion angle smaller than 90 degrees. The variations of SS bond length, SSS valence angle, and dihedral angle of Sn2- anions are related to the polarization of the lone pair and electronic charge of the anion by the electric field of the cations. A correlation between the torsion angle and the SSS valence angle is shown as that previously reported between the length of the bond around which the torsion takes place and the dihedral angle value. These geometry changes are explained by the hyperconjugation concept and the electron long-pair repulsion.     

A density functional theory investigation of Fe-N-O bonding in heme proteins and model systems

We report the results of a series of density functional theory (DFT) calculations of the M?ssbauer quadrupole splittings and isomer shifts in NO heme model compounds, together with the results of calculations of the M?ssbauer quadrupole splittings, isomer shifts, and electron paramagnetic resonance hyperfine coupling constants in a model Fe(II)(NO)(imidazole) complex as a function of Fe-NO bond length and Fe-N-O bond angle. The results of the M?ssbauer quadrupole splitting and isomer shift calculations on the NO heme model compounds show good accord between theory and experiment, with the largest errors being observed for structures having the largest crystallographic R(1) values. The results of the property surface calculations were then used to calculate Fe-NO bond length and Fe-N-O bond angle probability surfaces (Z-surfaces) for a nitrosyl hemoglobin, using, in addition, an energy filter. The results obtained yielded a most probable Fe-NO bond length (r) of 1.79 A and an Fe-N-O bond angle (beta) of 136 degrees -137 degrees. This bond length is somewhat longer than those observed in most model compounds but may be due, at least in part, to hydrogen bond formation with the distal His residue. Bond elongation was also observed in a geometry optimized Fe(II)(NO)(imidazole) complex hydrogen bonded to an imidazole residue, in which we find r = 1.76-1.78 A and beta = 137 degrees -138 degrees. The computed bond angles are close to the canonical approximately 140 degrees value found in most model systems. Highly bent Fe-N-O bond angles or very long Fe-NO bond lengths seem unlikely to occur in proteins, due to their high energies. We also investigated the molecular orbitals and spin densities in each of the six coordinate systems investigated and found the orbitals and spin densities to be generally similar those described previously for five coordinate systems. Taken together, these results show that M?ssbauer quadrupole splittings and isomer shifts, in addition to electron paramagnetic resonance hyperfine coupling constants, can now be calculated for nitrosyl heme systems with relatively good accuracy and that the results so obtained can be used to determine Fe-N-O geometries in metalloproteins. The Z-surface approach is thus applicable to both diamagnetic (CO) and paramagnetic (NO) heme proteins with in both cases the metal-ligand binding geometries found in the proteins being very close to those seen in model systems.     

棕色环反应产物中铁氧化态的讨论

The oxidation state of iron in the "brown-ring" reaction product[Fe(NO)(H₂O)₅]²⁺ and the bond between Fe and NO in this cation are discussed in detail. After presenting different views from the literature based on experimental evidences and theoretical calculations, the oxidation state of iron resonates between +2 and +3 inclining to +2. The Fe-N-O bond angle is 180°. In addition, we proposed an explanation for the slightly shortening of the bond length of NO after coordination to the iron ion.     

Bis(N-propyl-1,3-imidazolidine-2-thione)gold(I) chloride: Crystal and molecular structure

Summary The crystal and molecular structures of bis(N-propyl-1,3-imidazolidine-2-thione)gold(I) chloride, [(PrImt)₂Au]Cl, has been determined from three-dimensional x-ray intensity data collected on a CAD4 diffractometer. The compound crystallizes in the monoclinic space group P2₁/n witha=7.195(7),b=15.283(3),c=15.899(6) Å, =91.7(1) and Z = 4. Atomic parameters were refined by full-matrix least-squares methods to the R value of 6.2% for 2272 observed reflections. Gold(I) exhibits the usual linear coordination with S(1)-Au-S(10) angle of 177.7(1)°. The two [Prlmt] molecules are arranged intrans configuration which is attributed to the effects of intermolecular H-bonding between N-H and the halogen. The Au-S bond length is compared with the corresponding bond length in several known structures in order to evaluate thetrans influence of phosphorus, sulfur and chloride ligands on the Au-S bond.     

Approaches to ultimate functional polymers: quantum functional and molecular engineering materials

Both quantum functional material (Ψ‐engineering material) and molecular engineering materials are of interest as ultimate functional materials. The former creates a novel property which is specific to the structure, and the latter gives he functional material of the smallest size. In this paper, some aspects to construct those materials with polymer having big varieties and flexible applications are described: 1. Conjugating polymer superlattice (conjugating polymer multilayers which is able to change wave length of emission light). 2. Porphyrin arrays connected with molecular wires (a proto‐type photo‐information housing‐in and reading out polymeric material). 3. Oligonucleotide shackled with porphyrin (an artificial restrictive photoactive enzyme).     

THEORY OF INTRAMOLECULAR ORIENTATIONAL ORDER OF MESOGENIC UNITS IN MC-LCPS AND ITS APPLICATION

New concepts such as intramolecular orientational order parameter and corresponding model as well as theory were proposed to describe the intramolecular orientation of mesogenic units in the liquid crystalline polymer chains. The relationship between the intramolecular orientational order parameter and the molecular geometrical parameters such as the bond angle, the bond rotational angle and the rotational potential energy of chemical bonds was deduced. A significant even-odd oscillation of the intramolecular orientational order parameter of LCPs with different length of flexible spacer was found and rationally related to even-odd zig-zag manner of transition properties The verification and application of the theory are also discussed. The isotropic transition temperature predicted by the theory is shown to be in favourable agreement with the experiments.     

On-line FT-Raman and dispersive Raman spectra database of artists’ materials (e-VISART database)

Raman spectroscopy has been widely applied in the analysis of different types of artwork. This technique is sensitive, reliable, non-destructive and can be used in situ. However, there are few references in the literature regarding specific Raman spectra libraries for the field of artwork analysis. In this paper, the development of two on-line databases with Fourier transform Raman (FT-Raman; 1064 nm) and dispersive Raman (785 nm) spectra of materials used in fine art is presented; both are implemented in the e-vibrational spectroscopic databases of artists materials database (e-VISART). The database provides not only spectra, but also information about each pigment. It must be highlighted that for each pigment or material several spectra are available from different dealers. Some of the FT-Raman spectra available in the e-VISART database have not been published until now. Some examples in which the e-VISART database has been successfully used are presented.     

How big are atoms in crystals?

Atoms and bonds are central concepts in structural chemistry, but neither are concepts that arise naturally from the physics of condensed phases. It is ironic that the internuclear distances in crystals that are readily measured depend on the sizes of atoms, but since atoms in crystals can be defined in many different ways, all of them arbitrary and often incompatible, there is no natural way to express atomic size. I propose a simple coherent picture of Atoms-in-Crystals which combines properties selected from three different physically sound definitions of atoms and bonds. The charge density of the free atom that is used to construct the procrystal is represented by a sphere of constant charge density having the quantum theory of atoms in molecules (QTAIM) bonded radius. The sum of these radii is equal to the bond length that correlates with the bond flux (bond valence) in the flux theory of the bond. The use of this model is illustrated by answering the question: How big are atoms in crystals? The QTAIM bonded radii are shown to be simple functions of two properties, the number of quantum shells in the atomic core and the flux of the bond that links neighbouring atoms. Various radii can be defined. The univalent bonded radius measures the intrinsic size of the atom and is the same for all cations in a given row of the periodic table, but the observed bonded radius depends also on the bond flux that reflects the chemical environment.     

Structure Recovery and Recycling of Used LiCoO2 Cathode Material

A large number of lithium batteries have been retiring from the market of energy storage. Thus, recycling of the used electrode materials is becoming urgent. In this study, an industrial machinery processing was used to recover the crystal structure of the waste LiCoO₂ materials with the combination of small-scale equipment repair technology. The results show that the crystal parameters of the repaired LiCoO₂ material become small, the unit cell volume is reduced, and the crystal structure tends to be stable. The Co−O bond length of 1.9134 nm, O−Co−O bond angle of 94.72°, the (003) interplanar spacing of 0.467 nm indicate the excellent recovery level of the repaired LiCoO₂. In addition, the electrochemical performance of the repaired LiCoO₂ material is greatly improved, compared with the waste material. The capacity of the repaired electrode material can be maintained at 120 mAh g⁻¹ after 100 cycles at the current density of 0.2C. The promising rate performance of the repaired electrode material demonstrates the stable structure. This research work provides a large-scale method for the direct recovery of LiCoO₂ with the reduction of unnecessary energy and reagent consumption, which will be beneficial to the environmental protection.