Bond Pattern Research Articles

Coherent polaron dynamics of electrons solvated in polar liquids.

An electron solvated in a polar liquid is an elementary quantum system with properties governed by electric interactions with a fluctuating molecular environment. In the prevailing single particle picture, the quantum ground and excited states are determined by a self-consistent potential, as defined by the particular local configuration of the solvation shell. This description neglects collective many-body excitations, which arise from the coupling of electronic degrees of freedom and nuclear motions of the environment. While recent experiments have demonstrated collective nonequilbrium electronic-nuclear motion, i.e. polaron excitations in liquid water, their relevance in the broader context of polar liquids has remained unexplored. Here, we study the nonequilibrium dielectric response of the, compared to water, less polar alcohols isopropanol, and ethylene glycol, that also display a different hydrogen bond pattern. We demonstrate that ultrafast relaxation of photogenerated electrons impulsively induces coherent charge oscillations, which persist for some 10ps. They emit electric waves in a frequency range from 0.1 to 2 THz, depending on electron concentration. Oscillation frequencies and line shapes are reproduced by a unified polaron picture for alcohols and water, which is based on a Clausius-Mossotti local field approach for the THz dielectric function. The analysis suggests a longitudinal character of many-body polaron excitations and a weak coupling to transverse excitations, supported by the underdamped character of charge oscillations. Polaron dynamics are governed by the long-range Coulomb interaction between an excess electron and several thousands of polar solvent molecules, while local electron solvation geometries play a minor role.

Crystal Engineering of Pharmaceutical Cocrystals in the Discovery and Development of Improved Drugs.

The subject of crystal engineering started in the 1970s with the study of topochemical reactions in the solid state. A broad chemical definition of crystal engineering was published in 1989, and the supramolecular synthon concept was proposed in 1995 followed by heterosynthons and their potential applications for the design of pharmaceutical cocrystals in 2004. This review traces the development of supramolecular synthons as robust and recurring hydrogen bond patterns for the design and construction of supramolecular architectures, notably, pharmaceutical cocrystals beginning in the early 2000s to the present time. The ability of a cocrystal between an active pharmaceutical ingredient (API) and a pharmaceutically acceptable coformer to systematically tune the physicochemical properties of a drug (i.e., solubility, permeability, hydration, color, compaction, tableting, bioavailability) without changing its molecular structure is the hallmark of the pharmaceutical cocrystals platform, as a bridge between drug discovery and pharmaceutical development. With the design of cocrystals via heterosynthons and prototype case studies to improve drug solubility in place (2000-2015), the period between 2015 to the present time has witnessed the launch of several salt-cocrystal drugs with improved efficacy and high bioavailability. This review on the design, synthesis, and applications of pharmaceutical cocrystals to afford improved drug products and drug substances will interest researchers in crystal engineering, supramolecular chemistry, medicinal chemistry, process development, and pharmaceutical and materials sciences. The scale-up of drug cocrystals and salts using continuous manufacturing technologies provides high-value pharmaceuticals with economic and environmental benefits.

Ambiguous structure determination from powder data: four different structural models of 4,11-di-fluoro-quinacridone with similar X-ray powder patterns, fit to the PDF, SSNMR and DFT-D.

Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-di-fluoro-quinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z', molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.

Quantifying the Contribution of the Dispersion Interaction and Hydrogen Bonding to the Anisotropic Elastic Properties of Chitin and Chitosan.

The elastic tensors of chitin and chitosan allomorphs were calculated using density functional theory (DFT) with and without the dispersion correction and compared with experimental values. The longitudinal Young's moduli were 114.9 or 126.9 GPa for α-chitin depending on the hydrogen bond pattern: 129.0 GPa for β-chitin and 191.5 GPa for chitosan. Furthermore, the moduli were found to vary between 17.0 and 52.8 GPa in the transverse directions and between 2.2 and 15.2 GPa in shear. Switching off the dispersion correction led to a decrease in modulus by up to 63%, depending on the direction. The transverse Young's moduli of α-chitin strongly depended on the hydroxylmethyl group conformation coupled with the dispersion correction, suggesting a synergy between hydrogen bonding and dispersion interactions. The calculated longitudinal Young's moduli were, in general, higher than experimental values obtained in static conditions, and the Poisson's ratios were lower than experimental values obtained in static conditions.

Numerical issues on brittle shear failure of pier-wall continuous vertical joints in URM dutch buildings

Terraced houses built in the Netherland after 1980 are often characterized by the use of large units connected at corners by continuous thin layer mortar joints. Unlike the running bond pattern, usually modelled as a rigid connection, the vertical continuous connection may fail in shear and influence the global seismic capacity of the entire building. This work aims at investigating and comparing different numerical modelling approaches for simulating the vertical connections. Two different constitutive models are adopted to simulate the quasi-brittle nonlinear behaviour of the continuous joint, and their advantages and limitations are pointed out in terms of robustness and accuracy. The study considers both the component level in terms of U-shaped pier-wall configuration, and the full-scale structural level in terms of the global capacity for a two-storey masonry house assemblage, characterized by a running bond arrangement. The results of this work show that the shear failure involving the continuous joint usually reduces the strength capacity of the structure. Both the selection of constitutive models for the connection interface and masonry material are demonstrated to affect the results significantly. Decoupled direct traction-displacement relations for the interfaces appear to provide more robust results than coupled plasticity-based Coulomb friction laws. The selection of either a pre-fixed orthotropic smeared crack model for the masonry or a standard isotropic concrete-like rotating smeared crack formulation is demonstrated to strongly influence the activation of the different failure mechanisms and hence the response of the structure.

Synthesis and magnetic properties of two cobalt-coordination polymers containing 1,10-phenanthroline and alkyl dicarboxylates ligands

The structural and magnetic properties of two novel one-dimensional coordination compounds were investigated in the solid crystalline state to support studies of their potential as multifunctional materials. The new compounds are based on Co(II) and are named {[Co4(glu)4(phen)4(H2O)2]·H2O}n(1) and {[Co2(azl)2(phen)2(H2O)2]}n(2) (glu = glutarate, azl = azelate, and phen = 1,10-phenanthroline). Compound (2) is the first crystal structure of a cobalt-based coordination polymer with the mixed ligands azl and phen. The crystal structures of the compounds were determined by single crystal X-ray diffraction; where the influence of the alkyl dicarboxylates on the formation of a 1D looped or a single chain coordination polymer was observed. The FT-IR analysis confirms the coordination modes adopted by the mixed ligands azl and phen and the thermal analysis suggests some thermal stability up to 150-200 °C. Supramolecular analysis suggests an important role of the non-conventional C(sp2)-H···O hydrogen bond patterns in the crystals. Finally, weak antiferromagnetic interactions were observed in both complexes.

Valence-bond solid to antiferromagnet transition in the two-dimensional Su-Schrieffer-Heeger model by Langevin dynamics

Electron-phonon coupling is typically not associated with magnetic order but with either charge density waves (patterns of high and low electron density) or valence-bond solids (patterns of strong and weak electronic bonds). Using quantum Monte Carlo simulations, the authors demonstrate that, within the paradigmatic two-dimensional Su-Schrieffer-Heeger model, the electron-phonon interaction favors antiferromagnetic order in large regions of the phase diagram. A valence-bond solid is observed in the adiabatic regime, while the two phases are connected by an apparently direct phase transition.

Xylan adsorption on cellulose: Preferred alignment and local surface immobilizing effect

Interaction between xylan and cellulose microfibrils is required to maintain the integrity of secondary cell walls. However, the mechanisms governing their assembly and the effects on cellulose surface polymers are not fully clear. Here, molecular dynamics simulations are used to study xylan adsorption onto hydrated cellulose fibrils. Based on multiple spontaneous adsorption simulations it is shown that an antiparallel orientation is thermodynamically preferred over a parallel one, and that adsorption is accompanied by the formation of regular but orientation-dependent hydrogen bond patterns. Furthermore, xylan adsorption restricts the local dynamics of the adjacent glucose residues in the surface layer to a level of the crystalline core, which is manifested as a three-fold increase in their 13C NMR T1 relaxation time. These results suggest that xylan forms a rigid and ordered layer around the cellulose fibril that functions as a transition phase to more flexible and disordered polysaccharide and lignin domains.

Joint Layout Design: Finding the Strongest Connections within Segmental Masonry Arched Forms

Segmental arched forms composed of discrete units are among the most common construction systems, ranging from historic masonry vaults to contemporary precast concrete shells. Simple fabrication, transport, and assembly have particularly made these structural systems convenient choices to construct infrastructures such as bridges in challenging environmental conditions. The most important drawback of segmental vaults is basically the poor mechanical behaviour at the joints connecting their constituent segments. The influence of the joint shape and location on structural performances has been widely explored in the literature, including studies on different stereotomy, bond patterns, and interlocking joint shapes. To date, however, a few methods have been developed to design optimal joint layouts, but they are limited to extremely limited geometric parameters and material properties. To remedy this, this paper presents a novel method to design the strongest joint layout in 2D arched structures while allowing joints to take on a range of diverse shapes. To do so, a masonry arched form is represented as a layout of potential joints, and the optimization problems developed based on the two plastic methods of classic limit analysis and discontinuity layout optimization find the joint layout that corresponds to the maximum load-bearing capacity.

Various bond interactions between NO and anionic gold clusters: a theoretical calculation.

We studied the electronic and geometrical structures of AunNO- (n = 1-20) using the B3LYP method with relatively large basis sets to understand the size-dependent reactivities of Aun- with NO in recent experiments. In most cases, the Aun- in a AunNO- maintains its original geometries, and NO bonds with one gold atom in the N-atop pattern. The theoretical adsorption energy of NO in an even-sized AunNO- is generally larger than those in its odd-sized neighbors, which is consistent with the observed even-odd oscillation in experiments. Various bond interactions are identified between Aun- and NO according to analyses on the NO bond lengths, NO stretching frequencies, charge transfer extents, and densities of states of AunNO-. For the odd-sized AunNO- in their doublet states, the bonds between Aun- and NO can be described as weak dative bonds in the small size range, or even weaker electrostatic interactions for the large ones. For the even-sized AunNO- in their triplet states (with the exception of Au10NO- and Au16NO-), the electron transfer from Aun- to NO forms a triplet NO- and a neutral Aun, which bind together mainly through electrostatic interactions. The lowest-lying structures of Au10NO- and Au16NO- are in their singlets, and the bonds between NO and their gold parts can be described as polar covalent bonds. The stabilities of these two exceptional complexes are enhanced by the closed electron shells formed on their gold parts.

Synthesis of the extracellular domain of GLP-1R by chemical and biotechnological approaches.

The extracellular domain of the glucagon-like peptide-1 receptor, GLP-1R, is responsible for the binding of GLP-1, and a handful of additional agonists (such as exenatide, lixisenatide, and liraglutide) used daily for treating type II diabetes mellitus. Lead discovery and optimization, however, require binding studies, which, in turn, necessitate the total synthesis of GLP-1R, comprising 108 residues. A protein domain of 10–15 kDa size could be obtained either by expression in E. coli or by ligating solid-phase peptide synthesis (SPPS)-made fragments. However, direct overexpression fails to give a properly folded protein, as GLP-1R forms an inclusion body, which fails to refold due to improper disulfide pairing. Several bacterial strains, constructs, and fusion partners were probed and it was found that only co-expression with MBP gave a 3D-fold allowing the native disulfide bond pattern formation. Some fusion partners can act as covalently linked or in situ chaperones for guiding the refolding of GLP-1R toward success. Therefore, the bottleneck to preparing GPCR extracellular domains is the correct pairing of the Cys residues. As a proof-of-concept model, nGLP1-R was made by SPPS to form the purified full-length polypeptide chain, subjected to self-guided or spontaneous Cys pairing. However, the formation of correct SS-pairs was lagging behind any protocol in use support, and the bottleneck of large-scale protein production relies on the risky step of proper refolding, which is sometimes possible only if a suitable fusion partner effectively helps and catalysis of the correct disulfide formation.

The long-awaited synthesis and self-assembly of a small rigid C3-symmetric trilactam.

The challenging synthesis of a fused C3-symmetric trilactam (1) was executed in racemic and enantiomerically pure form. The rigidity, symmetry and high density of hydrogen bonding motifs make 1 an attractive candidate for self-assembly study, which revealed different hydrogen bond patterns in the crystals of rac-1-d3 and (+)-(SSS)-1.

Offsets between hyperconjugations, p→d donations and Pauli repulsions impact the bonding of E-O-E systems. Case study on elements of Group 14.

The nature of the E-O chemical bond (E = C, Si, Ge, Sn) is investigated in a wide range of model derivatives, such as oxonium cations, hydrogenated/methylated/fluorinated/chlorinated ethers and acyclic oligomers incorporating the E-O-E moiety. By means of density functional theory (DFT) calculations and natural bond orbital (NBO) techniques, we propose a bonding mechanism that explains the structural contrast between the organic and the inorganic counterparts of all these derivatives: the interplay between stabilizing interactions like LP(O)→σ*(E-X) hyperconjugations and LP(O)→d(E) donations with LP(O)⋯σ(E-X) vicinal Pauli repulsions (X = H, C, O, F, Cl) dictates the equilibrium structures in terms of E-O-E angles and E-O bond lengths. In addition, the present work represents the first study of oxonium ions that describes the structural discrepancies among organic derivatives and their heavier analogues. Another novel outcome for ethers and oligomers is that the two non-equivalent lone pair electrons (LPs) at the oxygen atoms impact in different manners the geometries of such derivatives, i.e. the s/p LP is correlated with the bending behaviour of the E-O-E units, while the pure p LP mainly dictates the short E-O bond distances of inorganic derivatives. Lastly, we evaluate the impact of the number of electronegative substituents, e.g. F, Cl or OEH3 groups, on the bond patterns developed for hydrogenated or methylated ethers.

Numerical analysis of the brick shape and bond pattern effects on the masonry cyclic behavior: a new brick shape to improve the masonry seismic performance

Numerical analysis of the brick shape and bond pattern effects on the masonry cyclic behavior: a new brick shape to improve the masonry seismic performance

Psychological Constructs and Dysfunctional Eating in Pakistani University Students

The present study aims to test a model that seeks to explain how Parental Bonding and Loneliness may be responsible in the development of Dysfunctional Eating Patterns such as Cognitive Restraint, Emotional Eating, Uncontrolled Eating, Drive toward Thinness, Bulimia and Dissatisfaction with Body Image. It was further hypothesized that Metacognitions, Core beliefs and Meta-Emotions would mediate between Loneliness, Parental Bonding, and the aforementioned Dysfunctional Eating Patterns. Correlational research design has been used. A sample of 210 university students was selected from government and private universities. Urdu translated versions of UCLA Loneliness Scale (Version 3), Three Factor Eating Questionnaire-R-18, Eating Disorders Inventory-3, Parental Bonding Inventory, Beliefs about Emotions Scale, Eating Disorders Belief Questionnaire and Metacognitions Questionnaire were used for assessment purposes. Correlational Analysis, and Multiple Hierarchical Regression were used to analyze the data. Almost all dimensions of Parental Bonding showed significant relationship with some patterns of Dysfunctional Eating. Loneliness did not show any significant correlation with Dysfunctional Eating. None of the hypothesized mediators(Metacognitions, Meta-Emotions and Core Beliefs) mediated the relationship between Parental Bonding dimensions and patterns of Dysfunctional Eating, yet some interesting relationships emerged. The findings of this research can help in understanding the cultural differences between East and West. Possible reasons why results could not support the previous literature are discussed.  

Hydrogen Bond Patterns of Dipyridone and Bis(Hydroxypyridinium) Cations.

Dipyridonyl-substituted derivatives 2–4 of benzene, pyridine, and pyrazine, respectively, were synthesized to examine the ability of 2-pyridone and its protonated species to direct the self-assembly by hydrogen bonding. Structural analysis by single-crystal X-ray diffraction (SCXRD) of 2 and 4 in trifluoroacetic acid demonstrated that salts are formed as a result of the transfer of protons from the acid to the base (organic species) to generate a bis(hydroxypyridinium) dication. However, if no proton transfer takes place like in the case of crystals of 3 grown from DMSO/H2O, the self-assembly is mainly directed by the typical R22(8) hydrogen bond motif of 2-pyridone. These results indicate that the process of converting a neutral 2-pyridonyl group into a hydroxypyridinium cation makes structure prediction difficult. Consequently, examination of proton transfer and assembly of dipyridone and its protonated species are of interest. In combination with SCXRD, Hirshfeld surface analysis (HSA) was also used to have a better understanding on the nature of intermolecular interactions within crystal structures of 2–4. The large number of F···H/H···F, H···O/O···H, H···H, and H···C/C···H contacts revealed by HSA indicates that hydrogen bonding and van der Waals interactions mainly contribute to crystal packing.

Electronegativity under Confinement.

The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree–Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures.

Correlation Effects in Trimeric Acylphloroglucinols

Trimeric acylphloroglucinols (T-ACPLs) are a subclass of the large class of acylphloroglucinols—derivatives of 1,3,5-trihydroxybenzene containing an R–C=O group. T-ACPL molecules contain three acylphloroglucinol moieties linked by methylene bridges. Many of them are present in natural sources and exhibit biological activities, often better than the corresponding activities of monomeric acylphloroglucinols. All the stable conformers of T-ACPLs contain seven intramolecular hydrogen bonds, which constitute the dominant stabilising factors. A total of 38 different T-ACPLs, including both naturally occurring and model molecules, have been calculated at the HF and DFT/B3LYP levels. The DFT/B3LYP calculations were carried out both without and with Grimme’s dispersion correction, to highlight the dispersion (and, therefore, also electron correlation) effects for these molecules. The roles of dispersion are evaluated considering the effects of Grimme’s correction on the estimation of the conformers’ energies, the description of the characteristics of the individual hydrogen bonds, the conformers’ geometries and other molecular properties. Overall, the results offer a comprehensive overview of the conformational preferences of T-ACPL molecules, their intramolecular hydrogen bond patterns, and the correlation effects on their properties.

Synthesis, crystal structure, hydrogen bond patterns and Hirshfeld surface analysis of (S)-5-(4-hydroxybenzyl)-imidazolidine-2,4‑dione

The title compound, (S)-5-(4-hydroxybenzyl)-imidazolidine-2,4‑dione, a new α-amino acid hydantoin derivative with formula C10H10N2O3 has been synthesized and structurally characterized by MS, FT-IR, NMR, and X-ray diffraction techniques. Spectroscopy results are consistent with the skeleton structure. The powder X-ray diffraction data confirms the phase purity of the crystalline sample. Single-crystal X-ray diffraction analysis indicated that crystallizes in the orthorhombic space group P212121 (N°19), Z = 4, and unit cell parameters a = 6.217(3) Å, b = 7.653(3) Å, c = 19.824(8) Å. The molecular structure and crystal packing are stabilized by intermolecular N–H···O and O–H···O hydrogen formed infinite two-dimensional chains, with graph-set C(6), C(5) and C(11) that run along the a, b and c directions forming a two-dimensional network. Hirshfeld surface analysis confirm that the most important contributions for the crystal packing are from N–H··O and O–H··O interactions. Energy framework calculations suggest that the contacts formed between molecules are slightly electrostatic and revealed that interactions exhibit approximately complex zig-zag shape topology in the crystal structure.

Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction.

A neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs, and increased significantly after the animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, the solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy, revealing that it has an N-terminal tail, three α-helices (α2, Gly9−Asn28; α3, His34−Gly38; and α5, Glu62−Arg72), and a π-helix (π4, Cys43−Tyr54), and is structurally constrained by a pattern of disulfide bonds (Cys7–Cys43, Cys23–Cys39, and Cys26–Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substitution, and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, and G73) are located at either end of the sequence, which are sterically close to each other and presumably constitute the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily, revealing a folding pattern, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand–receptor binding specificity.