Kink Sites Research Articles

Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.

Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO)3-GPOALO-(GPO)4 to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.

Phase Stability and Anisotropic Sublimation of Cubic Ge–Sb–Te Alloy Observed by In Situ Transmission Electron Microscopy

Phase stability and anisotropic sublimation dynamics of the cubic Ge–Sb–Te alloy have been investigated by in situ transmission electron microscopy (TEM). The starting point of the phase-transition study is an epitaxially aligned Ge1Sb2Te4 grain on a Si(111) substrate. Upon in situ heating, the cubic phase remains stable up to the sublimation point without a transition to the thermodynamically stable trigonal crystal structure which is attributed to Si diffusion into the Ge1Sb2Te4 grain. The sublimation process is made visible with atomic resolution. The anisotropic process leads to the formation of stable {111} facets via kink nucleation on stable steps and subsequent sublimation from those kink sites as predicated by the terrace-step-kink model. Kink nucleation sites are identified and are in accordance with the broken-bond model approach.

Nonequilibrium Kink Density from One-Dimensional Nucleation for Step Velocity Predictions

Crystal growth rates depend on the density of kink sites along step edges, ρ. The supersaturation-dependence of the kink density, ρ(S), is often ignored despite available nonequilibrium models for centrosymmetric crystals. The aim of this work is to derive ρ(S) from a rather simple one-dimensional nucleation framework in a manner that accounts for multiheight kinks. These become more prevalent at higher S and/or lower kink energies where the step front roughens (i.e., higher ρ). We arrive at a density of kinetic kinks that contribute to the step velocity and make comparisons with other models and simulations. Our model almost entirely eliminates systematic errors in predicted step velocities and crystal growth rates.

Ion dissolution mechanism and kinetics at kink sites on NaCl surfaces

Desolvation barriers are present for solute-solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na+ and Cl- are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion-crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.

Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.

The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.

The Effect of Additives on the Early Stages of Growth of Calcite Single Crystals

As crystallization processes are often rapid, it can be difficult to monitor their growth mechanisms. In this study, we made use of the fact that crystallization proceeds more slowly in small volumes than in bulk solution to investigate the effects of the soluble additives Mg2+ and poly(styrene sulfonate) (PSS) on the early stages of growth of calcite crystals. Using a “Crystal Hotel” microfluidic device to provide well‐defined, nanoliter volumes, we observed that calcite crystals form via an amorphous precursor phase. Surprisingly, the first calcite crystals formed are perfect rhombohedra, and the soluble additives have no influence on the morphology until the crystals reach sizes of 0.1–0.5 μm for Mg2+ and 1–2 μm for PSS. The crystals then continue to grow to develop morphologies characteristic of these additives. These results can be rationalized by considering additive binding to kink sites, which is consistent with crystal growth by a classical mechanism.

The Effect of Additives on the Early Stages of Growth of Calcite Single Crystals

AbstractAs crystallization processes are often rapid, it can be difficult to monitor their growth mechanisms. In this study, we made use of the fact that crystallization proceeds more slowly in small volumes than in bulk solution to investigate the effects of the soluble additives Mg2+ and poly(styrene sulfonate) (PSS) on the early stages of growth of calcite crystals. Using a “Crystal Hotel” microfluidic device to provide well‐defined, nanoliter volumes, we observed that calcite crystals form via an amorphous precursor phase. Surprisingly, the first calcite crystals formed are perfect rhombohedra, and the soluble additives have no influence on the morphology until the crystals reach sizes of 0.1–0.5 μm for Mg2+ and 1–2 μm for PSS. The crystals then continue to grow to develop morphologies characteristic of these additives. These results can be rationalized by considering additive binding to kink sites, which is consistent with crystal growth by a classical mechanism.

Crystallization of Aluminum Hydroxide in a Sodium Aluminate Solution on a Heterogeneous Surface

Aluminum hydroxide was crystallized in a sodium aluminate solution as bayerite at room temperature. Primary particles appeared as conical pyramids. They were born on particles of α-Al2O3 which had been preformed on a surface of FeCrAl alloy mesh as a result of its annealing. The primary nucleation was discussed using a two-step model that consists of a formation of prenucleation clusters and their transformation into nuclei. The induction period is an inversely proportional function to a square of the substrate surface and depends on its nature. Stirring the solution affected the primary nucleation preventing the formation of the prenucleation clusters. At an early stage, in a supersaturated state, the lateral surface of the primary pyramids grew via filling kink sites and forming the secondary pyramids. The secondary pyramids appeared from the prenucleation clusters. The pyramid base grew by a screw mechanism with an unwinding spiral. When a supersaturate degree of the solution decreased, the lateral sur...

Structural Motifs for Modeling Sulfur‐Poly(acrylonitrile) Composite Materials in Sulfur‐Lithium Batteries

AbstractKey structural motifs of cyclized‐poly(acrylonitrile) (PAN) and sulfur/PAN composite (SPAN) are identified and their energies are evaluated using density functional theory (DFT). Energetically favorable structural motifs are utilized to design smaller representative molecular models of both PAN and SPAN for in‐depth investigations. A zig‐zag configuration with multiple kink sites is energetically favorable for PAN materials, with the carbon kink site being the most reactive site. To form SPAN, sulfur binds to this kink site, resulting in structures typically containing S=C double bonds at kink sites and S chains that bridge between neighboring PAN fragments. It is found that the formation of large sulfur rings is possible because they are flexible enough to accommodate their length to the shape of the PAN fragment.

Role of Molecular Recognition in l-Cystine Crystal Growth Inhibition.

l-Cystine kidney stones—aggregates of single crystals of the hexagonal form of l-cystine—afflict more than 20 000 individuals in the United States alone. Current therapies are often ineffective and produce adverse side effects. Recognizing that the growth of l-cystine crystals is a critical step in stone pathogenesis, real-time in situ atomic force microscopy of growth on the (0001) face of l-cystine crystals and measurements of crystal growth anisotropy were performed in the presence of prospective inhibitors drawn from a 31-member library. The most effective molecular imposters for crystal growth inhibition were l-cystine mimics (aka molecular imposters), particularly l-cystine diesters and diamides, for which a kinetic analysis revealed a common inhibition mechanism consistent with Cabrera–Vermilyea step pinning. The amount of inhibitor incorporated by l-cystine crystals, estimated from kinetic data, suggests that imposter binding to the {0001} face is less probable than binding of l-cystine solute molecules, whereas imposter binding to {101̅0} faces is comparable to that of l-cystine molecules. These estimates were corroborated by computational binding energies. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and l-cystine crystal kink sites, and the inhibition of crystal growth. The observations are consistent with the reduction of l-cystine stone burden in mouse models by the more effective inhibitors, thereby articulating a strategy for stone prevention based on molecular design.

Elucidation of Active Sites for the Reaction of Ethanol on TiO2/Au(111)

Obtaining a molecular-level understanding of the reaction of alcohols with heterogeneous model catalysts is critical for improving industrial catalytic processes, such as the production of H2 from alcohols. Gold has been shown to be an excellent oxidation catalyst once oxygen is added to it. The use of reducible oxides provides a source of oxygen on Au(111) for the reaction of ethanol, which is easily regenerated in the presence of an oxygen background. In this work, ethanol operates as a probe molecule to investigate the role of Au(111), TiO2 nanoparticles, and TiO2/Au interfacial surface sites on the catalytic properties of TiO2/Au(111). Ultrahigh vacuum temperature-programmed desorption (TPD) studies with ethanol/Au(111) elucidate previously unreported adsorption sites for ethanol. Ethanol molecularly adsorbs to Au terrace sites, step edges, and undercoordinated kink sites with adsorption energies of −51.7, −55.8, and −65.1 kJ/mol, respectively. A TPD coverage study of ethanol on TiO2/Au(111) indicates ethanol undergoes dissociative adsorption to form H*(a) and CH3CH2O*(a) on the inverse model catalyst surface. The desorption temperature of low coverages of ethanol from TiO2/Au(111) (Tdes ≈ 235 K) is at an intermediate temperature between the desorption temperatures from bulk Au(111) and TiO2(110), indicating both Au and TiO2 play a role in the adsorption of ethanol. Both low-temperature adsorption and high-temperature reactions are studied and indicate that ethanol-derived products such as acetaldehyde and ethylene desorb from TiO2/Au(111) at ∼500 K. Herein, we report the identification of catalytically active sites on TiO2/Au(111) as interfacial sites between the oxide and Au(111) surface through the use of temperature-programmed desorption and infrared reflection absorption spectroscopy.

Two-Dimensional Nucleation on the Terrace of Colloidal Crystals with Added Polymers.

Understanding nucleation dynamics is important both fundamentally and technologically in materials science and other scientific fields. Two-dimensional (2D) nucleation is the predominant growth mechanism in colloidal crystallization, in which the particle interaction is attractive, and has recently been regarded as a promising method to fabricate varieties of complex nanostructures possessing innovative functionality. Here, polymers are added to a colloidal suspension to generate a depletion attractive force, and the detailed 2D nucleation process on the terrace of the colloidal crystals is investigated. In the system, we first measured the nucleation rate at various area fractions of particles on the terrace, ϕarea. In situ observations at single-particle resolution revealed that nucleation behavior follows the framework of classical nucleation theory (CNT), such as single-step nucleation pathway and existence of critical size. Characteristic nucleation behavior is observed in that the nucleation and growth stage are clearly differentiated. When many nuclei form in a small area of the terrace, a high density of kink sites of once formed islands makes growth more likely to occur than further nucleation because nucleation has a higher energy barrier than growth. The steady-state homogeneous 2D nucleation rate, J, and the critical size of nuclei, r*, are measured by in situ observations based on the CNT, which enable us to obtain the step free energy, γ, which is an important parameter for characterizing the nucleation process. The γ value is found to change according to the strength of attraction, which is tuned by the concentration of the polymer as a depletant.

Modeling Step Velocities and Edge Surface Structures during Growth of Non-Centrosymmetric Crystals

Almost all molecules are non-centrosymmetric, which produces interaction anisotropy within a crystal lattice. This anisotropy generates multiple types of kink sites on each crystal step and repeating patterns of rows with different growth units from the perspective of the lattice interaction environment, even for pure molecular crystals. As a result, unstable edge rows may be generated that dissolve under conditions of crystal growth. A method to account for edge surface structures, considering such effects, is required to accurately model the step velocity, which is vital for a mechanistic description of crystal growth. We classify both thermodynamic and kinetic contributions to step row instability and develop expressions for kink densities and step velocities that capture these important non-centrosymmetric phenomena. To demonstrate the utility of our framework, we consider in depth the case of an alternating-row A–B step. Our mechanistic predictions compare favorably to kinetic Monte Carlo simulations...

Revisiting CO Activation on Co Catalysts: Impact of Step and Kink Sites from DFT

Fischer–Tropsch synthesis of hydrocarbons from CO and H2 is an established industrial process, during which the C–O bond must break. The preferred mechanism and sites at which CO is activated and hydrocarbon products are formed remains under debate. Density functional theory calculations are used to investigate direct and H-assisted dissociation of CO at kink and step sites on FCC Co(321) and Co(221), at which direct dissociation is demonstrated to be intrinsically preferred at low coverage. The CO dissociation rate is predicted to be higher at defect sites than on extended facets on FCC Co, with dissociation at the kink site having the highest relative rate of all FCC Co site types predicted to be exposed on FCC Co nanocrystals. Nevertheless, the increase in activity is not sufficient to exceed that of highly active HCP Co sites. However, the intrinsically preferred mechanism of CO activation at low coverage, direct rather than H assisted, is concluded to be the same on FCC and HCP Co.

Steady State Morphologies of Paracetamol Crystal from Different Solvents

Nowadays, mastering crystal growth from different points of view is becoming an essential technique, with the continuous development of pharmaceutical industries and scientific research. Paracetamol (acetaminophen), a medication used to treat pain and fever, is often at a steady state growth shape but has a complex crystal habit. Because of its non-centrosymmetric structure, paracetamol has multiple types of kink sites on each edge of each face, which brings more difficulties in growth predicting for crystal morphology designers. Therefore, accurate analysis of paracetamol crystal structure and the ability to design its crystal shapes from as many solvents as possible are of significant meaning and interest. Here, a general mechanistic spiral growth model is introduced to predict the steady state morphologies of paracetamol crystal grown from 30 different solvents. An upgraded kink rate expression and a kink density expression are proposed to describe how the growth units associated with the kink, step, e...

Modeling the formation of TiO2 ultra-small nanoparticles.

The structures of TiO2 ultra-small nanoparticles (USNPs) at the atomistic level have been predicted because of their potential importance in catalytic, environmental, biological and energy applications. Low energy (TiO2)n clusters and USNPs (n up to 80 at the B3LYP/DZVP2 level, and up to 384 at the PM6 level) were found using a novel bottom-up global optimization approach that is based on all-atom real-space calculations. These structures include USNPs that belong to 1-D, 2-D and 3-D USNP series where all the members share the same fragment types and local translational symmetries. Most of the metastable 2-D and 3-D USNPs contain tubular building blocks similar to the 1-D USNPs. The 3-D USNPs that resemble the bulk anatase are predicted to be energetically favorable structures for 64 ≤ n ≤ 384. A fragment-based model was developed to relate the energy with geometry for the 1-D, 2-D and 3-D USNPs. Surface energy densities were predicted for surface fragments at the different positions of the USNPs using this new model. Based on the predicted surface energy densities and the partial density of states, the most catalytically active sites for the anatase-like 3-D USNPs were predicted to be the kink sites on Face-x surfaces consisting of an octahedral-Ti, the step (edge) sites between the Face-x and Face-y surfaces consisting of a square pyramidal-Ti (on Face-x), and the step sites consisting of a trigonal bipyramidal Ti on the Face-y surfaces.

Structure-sensitive enantiospecific adsorption on naturally chiral Cu(hkl)R&S surfaces

The desorption kinetics of a chiral compound, R-3-methylcyclohexanone (R-3MCHO), have been measured on both enantiomers of seven chiral Cu(hkl)R&S surfaces and on nine achiral Cu single crystal surfaces with surface structures that collectively span the various regions of the stereographic triangle. The naturally chiral surfaces have terrace-step-kink structures formed by all six possible combinations of the three low Miller index microfacets. The chirality of the kink sites is defined by the rotational orientation of the (1 1 1), (1 0 0) and (1 1 0) microfacets forming the kink. R-3MCHO adsorbs reversibly on these Cu surfaces and temperature programmed desorption has been used to measure its desorption energetics from the chiral kink sites. The desorption energies from the R- and S-kink sites are enantiospecific, , on the chiral surfaces. The magnitude of the enantiospecificity is ≈ 1 kJ mol−1 on all seven chiral surfaces. However, the values of are sensitive to elements of the surface structure other than just their sense of chirality as defined by the rotational orientation of the low Miller index microfacets forming the kinks; changes sign within the set of surfaces of a given chirality.

Morphology Controls on Calcite Recrystallization.

Environmental scientists and geoscientists working in different fields regard the reactivity of calcite and corresponding changes in its trace elemental- or isotopic composition from diametrically opposed points of view. As one extreme, calcite based environmental remediation strategies rely on the fast recrystallization of calcite and the concurrent uptake and immobilization of pollutants. Paleo-ecological investigations denote the other extreme, and rely on the invariability of calcite composition over geological periods of time. We use long-term radiotracer experiments to quantify recrystallization rates of seven types of calcite powder with diverse morphology and particle size distribution. On the one hand our results demonstrate the long-term metastability of calcite with equilibrated crystal surfaces even at isotopic dis-equilibrium. On the other hand, we document the extremely high reactivity and interfacial free energy of freshly ground, rough calcite. Our results indicate that bulk calcite recrystallization is an interfacial free energy driven Ostwald-ripening process, in which particle roughness effects dominate over the effect of crystal habitus and particle size. We confirm that the dynamic equilibrium exchange of crystal constituents between kink sites involves an activation barrier of about 25 kJ/mol. At room temperature the equilibrium exchange is limited to a near surface region and proceeds at a rate of (3.6 ± 1.4)·10-13 mol/(m2·s).

Synthesis of MgO nanocrystals with abundant surface defects via a carbonization method employing CO2 gas as starting material

Taking its unique property into consideration, uniformly dispersed MgO nanoparticles with abundant surface oxygen defects was primarily synthesized via a facile carbnization method employing CO2 gas as carburizer in this study. After reaction at 60°C for 2h, Mg2+ ions were totally carbonized to caterpillar-like Mg5(CO3)4(OH)2(H2O)4 precursor. And through decarbonization and dehydration processes during calcination, as-prepared Mg5(CO3)4(OH)2 (H2O)4 precursor with micro-nano structure was thouroughly converted to well-crystallized MgO nanospheres. As-evidenced by the UV–VIS-NIR diffuse reflectance spectroscopy, due to the largely intensified low-coordinated oxide ions at the corner and kink sites with decreasing the average size, the forbidden band gap of as-prepared MgO nanocrystals is 5.3eV, which thus endows it intriguing applications in different fields.

Dissociative Carbon Dioxide Adsorption and Morphological Changes on Cu(100) and Cu(111) at Ambient Pressures.

Ambient-pressure X-ray photoelectron spectroscopy (APXPS) and high-pressure scanning tunneling microscopy (HPSTM) were used to study the structure and chemistry of model Cu(100) and Cu(111) catalyst surfaces in the adsorption and dissociation of CO2. It was found that the (100) face is more active in dissociating CO2 than the (111) face. Atomic oxygen formed after the dissociation of CO2 poisons the surface by blocking further adsorption of CO2. This "self-poisoning" mechanism explains the need to mix CO into the industrial feed for methanol production from CO2, as it scavenges the chemisorbed O. The HPSTM images show that the (100) surface breaks up into nanoclusters in the presence of CO2 at 20 Torr and above, producing active kink and step sites. If the surface is precovered with atomic oxygen, no such nanoclustering occurs.