Crystallization of tetrahedral patchy particles in silico

We investigate the competition between glass formation and crystallization of open tetrahedral structures for particles with tetrahedral patchy interactions. We analyze the outcome of such competition as a function of the potential parameters. Specifically, we focus on the separate roles played by the interaction range and the angular width of the patches, and show that open crystal structures (cubic and hexagonal diamond and their stacking hybrids) spontaneously form when the angular width is smaller than about 30°. Evaluating the temperature and density dependence of the chemical potential of the fluid and of the crystal phases, we find that adjusting the patch width affects the fluid and crystal in different ways. As a result of the different scaling, the driving force for spontaneous self-assembly rapidly grows as the fluid is undercooled for small-width patches, while it only grows slowly for large-width patches, in which case crystallization is pre-empted by dynamic arrest into a network glass.     

Estimation of the nucleation and crystal growth contributions to the overall crystallization energy barrier

Classical kinetic theories of polymer crystallization were applied to isothermal crystallization kinetics data obtained by polarized optical microscopy (PLOM) and differential scanning calorimetry (DSC). The fitted parameters that were proportional to the energy barriers obtained allow us to quantitatively estimate the nucleation and crystal growth contributions to the overall energy barrier associated to the crystallization process. It was shown that the spherulitic growth rate energy barrier found by fitting PLOM data is almost identical to that obtained by fitting the isothermal DSC crystallization data of previously self‐nucleated samples. Therefore, we demonstrated that by self‐nucleating the material at the ideal self‐nucleation (SN) temperature, the primary nucleation step can be entirely completed and the data obtained after subsequent isothermal crystallization by DSC contains only contributions from crystal growth or secondary nucleation. In this way, by employing SN followed by isothermal crystallization, we propose a simple method to obtain separate contributions of energy barriers for primary nucleation and for crystal growth, even in the case of polymers where PLOM data are very difficult to obtain (because they exhibit very small spherulites). Comparing the results obtained with poly(p‐dioxanone), poly(ε‐caprolactone), and a high 1,4 model hydrogenated polybutadiene, we have interpreted the differences in primary nucleation energy barriers as arising from differences in nuclei density. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1478–1487, 2008     

Spinodal for the solution-to-crystal phase transformation

The formation of crystalline nuclei from solution has been shown for many systems to occur in two steps: the formation of quasidroplets of a disordered intermediate, followed by the nucleation of ordered crystalline embryos within these droplets. The rate of each step depends on a respective free-energy barrier and on the growth rate of its near-critical clusters. We address experimentally the relative significance of the free-energy barriers and the kinetic factors for the nucleation of crystals from solution using a model protein system. We show that crystal nucleation is 8-10 orders of magnitude slower than the nucleation of dense liquid droplets, i.e., the second step is rate determining. We show that at supersaturations of three or four k(B)T units, crystal nuclei of five, four, or three molecules transform into single-molecule nuclei, i.e., the significant nucleation barrier vanishes below the thermal energy of the molecules. We show that the main factor, which determines the rate of crystal nucleation, is the slow growth of the near-critical ordered clusters within the quasidroplets of the disordered intermediate. Analogous to the spinodal in supersaturated fluids, we define a solution-to-crystal spinodal from the transition to single-molecule crystalline nuclei. We show that heterogeneous nucleation centers accelerate nucleation not only because of the wettinglike effects that lower the nucleation barrier, as envisioned by classical theory, but by helping the kinetics of growth of the ordered crystalline embryos.     

Pore nucleation in mechanically stretched bilayer membranes

We report a computer-simulation study of the free-energy barrier for the nucleation of pores in the bilayer membrane under constant stretching lateral pressure. We find that incipient pores are hydrophobic but as the lateral size of the pore nucleus becomes comparable with the molecular length, the pore becomes hydrophilic. In agreement with previous investigations, we find that the dynamical process of growth and closure of hydrophilic pores is controlled by the competition between the surface tension of the membrane and the line tension associated with the rim of the pore. We estimate the line tension of a hydrophilic pore from the shape of the computed free-energy barriers. The line tension thus computed is in a good agreement with available experimental data. We also estimate the line tension of hydrophobic pores at both macroscopic and microscopic levels. The comparison of line tensions at these two different levels indicates that the "microscopic" line tension should be carefully distinguished from the "macroscopic" effective line tension used in the theoretical analysis of pore nucleation. The overall shape of the free-energy barrier for pore nucleation shows no indication for the existence of a metastable intermediate during pore nucleation.     

Thermodynamics and kinetics of bubble nucleation: Simulation methodology

The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.     

Thermodynamics of diamond nucleation on the nanoscale

To have a clear insight into the diamond nucleation upon the hydrothermal synthesis and the reduction of carbide (HSRC), we performed the thermodynamic approach on the nanoscale to elucidate the diamond nucleation taking place in HSRC supercritical-fluid systems taking into account the capillary effect of the nanosized curvature of the diamond critical nuclei, based on the carbon thermodynamic equilibrium phase diagram. These theoretical analyses showed that the nanosize-induced interior pressure of diamond nuclei could drive the metastable phase region of the diamond nucleation in HSRC into the new stable phase region of diamond in the carbon phase diagram. Accordingly, the diamond nucleation is preferable to the graphite phase formation in the competing growth between diamond and graphite upon HSRC. Meanwhile, we predicted that 400 MPa should be the threshold pressure for the diamond synthesis by HSRC in the metastable phase region of diamond, based on the proposed thermodynamic nucleation on the nanoscale.     

Monte Carlo simulation study of droplet nucleation

A new rigorous Monte Carlo simulation approach is employed to study nucleation barriers for droplets in Lennard-Jones fluid. Using the gauge cell method we generate the excess isotherm of critical clusters in the size range from two to six molecular diameters. The ghost field method is employed to compute the cluster free energy and the nucleation barrier with desired precision of (1-2)kT. Based on quantitative results obtained by Monte Carlo simulations, we access the limits of applicability of the capillarity approximation of the classical nucleation theory and the Tolman equation. We show that the capillarity approximation corrected for vapor nonideality and liquid compressibility provides a reasonable assessment for the size of critical clusters in Lennard-Jones fluid; however, its accuracy is not sufficient to predict the nucleation barriers for making practical estimates of the rate of nucleation. The established dependence of the droplet surface tension on the droplet size cannot be approximated by the Tolman equation for small droplets of radius less than four molecular diameters. We confirm the conclusion of ten Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)] that integration of the normal component of the Irving-Kirkwood pressure tensor severely underestimates the nucleation barriers for small clusters.     

Crystal nucleation of colloidal hard dumbbells

Using computer simulations, we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases, and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned close-packed crystal structure is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.     

A qualitative picture of the barrier restricting rotation about single bonds

The simple model proposed is based on the repulsion between the four substituent or lone electron pairs of a tetrahedral atom and on the strongly anisotropic polarizability of the single bond. Bending back two electron pairs to form a double bond or a small ring, and the introduction of electronegative substituents, reduce the barrier.

A survey of known rotational barriers is given.     

Unprecedented differences in the diamond nucleation density between carbon- and silicon-faces of 4H-silicon carbides

4H-silicon carbides deposited by diamond films have wide applications in many fields such as semiconductor heterojunction, heat sink and mechanical sealing. Nucleation plays a critical role in the deposition of the diamond film on 4H-silicon carbides. Nevertheless, as a typical polar material, the fundamental mechanism of diamond nucleation on different faces of 4H-silicon carbides has not been fully understood yet. In this contribution, nucleation of diamond was performed on the carbon- and silicon-faces of 4H-silicon carbides in a direct current chemical vapor deposition device. The nucleation density on the carbon-face is higher by 2–3 orders of magnitude compared to the silicon-face. Transmission electron microscopy verifies that there are high density diamond nuclei on the interface between the carbon-face and the diamond film, which is different from columnar diamond growth structure on the silicon-face. Transition state theory calculation reveals that the unprecedented distinction of the nucleation density between the carbon-face and the silicon-face is attributed to different desorption rates of the absorbed hydrocarbon radicals. In addition, kinetic model simulations demonstrate that it is more difficult to form CH₂(s)-CH₂(s) dimers on silicon-faces than carbon-faces, resulting in much lower nucleation densities on silicon-faces.     

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopically encoded in the nucleobase sequences. Physically relevant interactions are considered explicitly, such as interchain excluded volume, anisotropic base-pairing and base-stacking, and single-stranded bending rigidity. The model is studied in detail by a specially adapted Monte Carlo simulation method, based on parallel tempering and biased trials, which is designed to overcome the entropic and enthalpic barriers associated with the sampling of hybridization events of multiple single-stranded chains in solution. This methodology addresses both the configurational complexity of bringing together two complementary strands in a favorable orientation (entropic barrier) and the energetic penalty of breaking apart multiple associated bases in a double-stranded state (enthalpic barrier). For strands with sequences restricted to nonstaggering association and homogeneous pairing and stacking energies, base-pairing is found to dominate the hybridization over the translational and conformational entropy. For strands with sequence-dependent pairing corresponding to that of DNA, the complex dependence of the model's thermal stability on concentration, sequence, and degree of complementarity is shown to be qualitatively and quantitatively consistent both with experiment and with the predictions of statistical mechanical models.     

Synthetic Semiconductor Diamond Electrodes: Comparison of Electrochemical Behavior of the Growth and Nucleation Surfaces of Thin Polycrystalline Films

A comparative study of electrochemical kinetics in ferro- and ferricyanide solutions is performed. Electrochemical impedance spectra for the growth and nucleation sides of relatively thin films of boron-doped polycrystalline diamond synthesized by hot-filament CVD technology are taken. Concentrations of noncompensated acceptor near the growth and nucleation surfaces are estimated. It is shown that the growth and nucleation surfaces differ little in their electrochemical behavior, which is attributed to the absence of significant difference in the concentration of electrochemically active structural defects or the boron-acceptor impurity between the two sides of thin diamond films.     

Vapor-to-droplet transition in a Lennard-Jones fluid: simulation study of nucleation barriers using the ghost field method

We report a comprehensive Monte Carlo (MC) simulation study of the vapor-to-droplet transition in Lennard-Jones fluid confined to a spherical container with repulsive walls, which is a case study system to investigate homogeneous nucleation. The focus is made on the application of a modified version of the ghost field method (Vishnyakov, A.; Neimark, A. V. J. Chem. Phys. 2003, 119, 9755) to calculate the nucleation barrier. This method allows one to build up a continuous trajectory of equilibrium states stabilized by the ghost field potential, which connects a reference droplet with a reference vapor state. Two computation schemes are employed for free energy calculations, direct thermodynamic integration along the constructed trajectory and umbrella sampling. The nucleation barriers and the size dependence of the surface tension are reported for droplets containing from 260 to 2000 molecules. The MC simulation study is complemented by a review of the simulation methods applied to computing the nucleation barriers and a detailed analysis of the vapor-to-droplet transition by means of the classical nucleation theory.     

Imaging SIMS for the investigation of substrate surfaces for CVD diamond deposition

The influence of substrate surface preparation on diamond nucleation is a major topic in the investigation of CVD-diamond deposition. The substrate, polishing material, its grain size, and the resulting surface roughness all influence diamond nucleation. Diamond can nucleate at scratches or residues of the polishing process which are providing nucleation sites. In this paper the surface of molybdenum and substrates polished with SiC and diamond powder was studied by imaging (2- and 3-dimensional) secondary ion mass spectrometry. The distribution and grain size of polishing residues (SiC, diamond) were determined and the reaction of diamond with the substrate during heating to deposition temperature was investigated. In this case a laterally inhomogeneous system of carbon containing species had to be characterized. Therefore compound-specific secondary ion mass spectrometry had to be performed. The results suggested that diamond residues on molybdenum substrates are partly dissolved during the heat treatment. The measurements indicate that a fraction of the diamond residues is still present after heat treatment and can provide nucleation sites for diamond deposition.     

On the coupling between slow diffusion transport and barrier crossing in nucleation

We model the coupling between slow diffusion transport and nucleation using the diffusion equation, an Ostwald-Freundlich boundary condition, and a mass balance linking nucleus size to flux across the nucleus-solution interface. The model retains some characteristics of the classical nucleation theory because of the common theoretical foundations behind classical nucleation theory and the Ostwald-Freundlich equation. For example, the classically critical-sized nucleus in the uniform supersaturated concentration field is an unstable equilibrium point. However, the model also shows that certain types of concentration profiles can drive a classically pre-critical nucleus over the nucleation barrier. We identify the separatrix as a function of both nucleus size and characteristics of the local concentration field. Our analysis may be useful for understanding the effects of local concentration fluctuations and especially for understanding the role of dense precursor particles in driving two-step nucleation processes. Our analysis may also provide a starting point for further statistical field theory analyses of local concentration fluctuations and their effects on nucleation rates.     

Nucleation in a simple model for protein solutions with anisotropic interactions

A lattice analog of density functional theory is used to explore the structural and thermodynamic properties of critical nuclei in mixtures of particles with attractive anisotropic interactions. Protein molecules are assumed to occupy the sites on a regular cubic lattice, with effective directional interactions that mimic hydrogen bonding and the solvation forces induced by water. Interaction parameters are chosen to qualitatively reproduce the phase behavior of protein solutions. Our model predicts that critical nuclei of the solidlike phase have nonspherical shapes, and that their specific geometry depends on the nature of the anisotropic interactions. Molecules tend to align in distinctive ways in the core and in the interfacial region of these critical clusters, and the width and structure of the interface are highly affected by the presence of a metastable fluid-fluid critical point. Close to the critical region, the height of the barrier to nucleation is strongly reduced; this effect is enhanced by increasing the anisotropy of the intermolecular interactions. Unlike systems with short-range isotropic interactions, nucleation in our model is initiated by highly ordered clusters in which the order-disorder transition is confined to the interfacial region.     

硼烯化学合成进展与展望

硼烯是由硼原子构成的单原子层厚的二维材料,具有丰富的化学和物理性质。本文集中介绍近年来硼烯在合成方面的理论与实验研究进展,重点分析基底、生长温度、生长前驱物等因素对硼成核选择性的影响,探讨能够促进硼烯成核的潜在方法。进一步将分析硼烯生长机制及理论研究方法,以此展望通过在基底上化学气相沉积合成硼烯的可能途径。本文旨在促进大面积、高质量硼烯样品的制备以推动硼烯的实际应用。     

Nucleation on active centers in confined volumes

Kinetic equations describing nucleation on active centers are solved numerically to determine the number of supercritical nuclei, nucleation rate, and the number density of nuclei for formation both of droplets from vapor and also crystalline phase from vapor, solution, and melt. Our approach follows standard nucleation model, when the exhaustion of active centers is taken into account via the boundary condition, and thus no additional equation (expressing exhaustion of active centers) is needed. Moreover, we have included into our model lowering of supersaturation of a mother phase as a consequence of the phase transition process within a confined volume. It is shown that the standard model of nucleation on active centers (Avrami approach) gives faster exhaustion of active centers as compared with our model in all systems under consideration. Nucleation rate (in difference to standard approach based on Avrami model) is equal to the time derivative of the total number of nuclei and reaches some maximum with time. At lower nucleation barrier (corresponding to higher initial supersaturation or lower wetting angle of nucleus on the surface of active center) the exhaustion of active centers is faster. Decrease in supersaturation of the mother phase is faster at higher number of active centers.     

Quantum chemical study of penicillin: Reactions after acylation

The density functional theory methods were used on the model molecules of penicillin to determine the possible reactions after their acylation on β‐lactamase, and the results were compared with sulbactam we have studied. The results show that, the acylated‐enzyme tetrahedral intermediate can evolves with opening of β‐lactam ring as well as the thiazole ring; the thiazole ring‐open products may be formed via β‐lactam ring‐open product or from tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. In virtue of the water‐assisted, their energy barriers are obviously reduced. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Nucleation in binary polymer blends: effects of foreign mesoscopic spherical particles

We study nucleation in binary polymer blends in the presence of mesoscopic spherical particles using self-consistent field theory, considering both heterogeneous and homogeneous nucleation mechanisms. Heterogeneous nucleation is found to be highly sensitive to surface selectivity and particle size, with rather subtle dependence on the particle size. Particles that preferentially adsorb the nucleating species generally favor heterogeneous nucleation. For sufficiently strong adsorption, barrierless nucleation is possible. By comparing the free energy barrier for homogeneous and heterogeneous nucleation, we construct a kinetic phase diagram.