A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.     

甘油对冰晶生长抑制作用的分子动力学模拟

采用分子模拟方法研究了正交晶系冰晶(020)生长面在不同浓度甘油水溶液中的生长情况. 通过统计分析氢键数、 密度分布函数、 均方根偏差和原子间径向分布函数研究了水分子和甘油分子的动态行为. 结果表明, 甘油分子在水溶液中可与水分子形成大量氢键, 这使水分子间的氢键作用受到抑制, 降低了水分子的扩散性, 致使冰晶不易成核和生长; 另外, 一些甘油分子可代替水分子吸附在晶面上, 甚至占据晶格位点, 这种行为打破了冰晶的对称性并且降低了冰晶的生长速率. 因此, 甘油可同时在晶面和液相中抑制冰晶的生长.     

A powerful computational crystallography method to study ice polymorphism

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction potential for oxygen and hydrogen in bulk water, derived from neutron scattering data, able to successfully describe complex phenomena such as proton hopping and bond formation/breaking. The present study demonstrates the ability of the interaction potential model to well describe most ice structures found in the phase diagram of water and to estimate the relative stability of 16 known phases through a cluster analysis of simulated powder diagrams of polymorphs obtained from MD simulations. The proposed computational protocol is suited for automated crystal structure identification.     

Crystal packing in a solvent-free or chloroform-solvated dinuclear platinum(III) organometallic complex

The synthesis and crystal structure determination of the dinuclear organometallic platinum(III) complex [Pt(2-phenylpyridine)(2-mercaptothiazoline)(Cl)]₂ and its solvate [Pt(2-phenylpyridine)(2-mercaptothiazoline)(Cl)]₂·3CHCl₃ have been performed. Both crystals present a layered structure in which the molecules of the complex are held together by weak intermolecular interactions. In the solvated crystal, the chloroform molecules are arranged in extended 2D planar layers between the molecular layers.     

Anisotropy in the crystal growth of hexagonal ice, I(h)

Growth of ice crystals has attracted attention because ice and water are ubiquitous in the environment and play critical roles in natural processes. Hexagonal ice, I(h), is the most common form of ice among 15 known crystalline phases of ice. In this work we report the results of an extensive and systematic molecular dynamics study of the temperature dependence of the crystal growth on the three primary crystal faces of hexagonal ice, the basal {0001} face, the prism {1010} face, and the secondary prism {1120} face, utilizing the TIP4P-2005 water model. New insights into the nature of its anisotropic growth are uncovered. It is demonstrated that the ice growth is indeed anisotropic; the growth and melting of the basal face are the slowest of the three faces, its maximum growth rates being 31% and 43% slower, respectively, than those of the prism and the secondary prism faces. It is also shown that application of periodic boundary conditions can lead to varying size effect for different orientations of an ice crystal caused by the anisotropic physical properties of the crystal, and results in measurably different thermodynamic melting temperatures in three systems of similar, yet moderate, size. Evidence obtained here provides the grounds on which to clarify the current understanding of ice growth on the secondary prism face of ice. We also revisit the effect of the integration time step on the crystal growth of ice in a more thorough and systematic way. Careful evaluation demonstrates that increasing the integration time step size measurably affects the free energy of the bulk phases and shifts the temperature dependence of the growth rate curve to lower temperatures by approximately 1 K when the step is changed from 1 fs to 2 fs, and by 3 K when 3 fs steps are used. A thorough investigation of the numerical aspects of the simulations exposes important consequences of the simulation parameter choices upon the delicate dynamic balance that is involved in ice crystal growth.     

On the definition of a Monte Carlo model for binary crystal growth

We show that consistency of the transition probabilities in a lattice Monte Carlo (MC) model for binary crystal growth with the thermodynamic properties of a system does not guarantee the MC simulations near equilibrium to be in agreement with the thermodynamic equilibrium phase diagram for that system. The deviations remain small for systems with small bond energies, but they can increase significantly for systems with large melting entropy, typical for molecular systems. These deviations are attributed to the surface kinetics, which is responsible for a metastable zone below the liquidus line where no growth occurs, even in the absence of a 2D nucleation barrier. Here we propose an extension of the MC model that introduces a freedom of choice in the transition probabilities while staying within the thermodynamic constraints. This freedom can be used to eliminate the discrepancy between the MC simulations and the thermodynamic equilibrium phase diagram. Agreement is achieved for that choice of the transition probabilities yielding the fastest decrease of the free energy (i.e., largest growth rate) of the system at a temperature slightly below the equilibrium temperature. An analytical model is developed, which reproduces quite well the MC results, enabling a straightforward determination of the optimal set of transition probabilities. Application of both the MC and analytical model to conditions well away from equilibrium, giving rise to kinetic phase diagrams, shows that the effect of kinetics on segregation is even stronger than that predicted by previous models.     

Growth and Dissolution of Organic Crystals with “Tailor-Made” Inhibitors—Implications in Stereochemistry and Materials Science

When crystals of organic compounds are grown in the presence of growth inhibitors, there is a change in crystal morphology. A stereochemical correlation exists between the crystal structure, its modified morphology, and the molecular structure of the inhibitor. This correlation has been successfully exploited for the efficient resolution of conglomerates, the engineering of organic crystals with desired morphologies, the direct and relative assignment of the absolute configurations of chiral molecules and crystals, and for the design of a new model for the spontaneous generation of optical activity. In an analogous way dissolution of organic crystals in the presence of these growth inhibitors induces etch pits at preselected faces. The effect of solvent on crystal growth has been analyzed in some model systems. The experimental results are complemented by atom-atom potential energy calculations.     

A general set of order parameters for molecular crystals

Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.     

Nonspherical colloidal crystals fabricated by the thermal pressing of colloidal crystal chips

Nonspherical colloids and their ordered arrays may be more attractive in applications such as photonic crystals than their spherical counterparts because of their lower symmetries, although such structures are difficult to achieve. In this letter, we describe the fabrication and characterization of colloidal crystals constructed from nonspherical polyhedrons. We fabricated such nonspherical colloidal crystals by pressing spherical polymer colloidal crystal chips at a temperature slightly lower than the glass-transition temperature (T(g)) of these polymer colloids. During this process, the polymer microspheres were distinctively transformed into polyhedrons according to their crystal structures, whereas the long-range order of the 3D lattice was essentially preserved. Because a working temperature lower than T(g) effectively prevented the colloidal crystals from fusing into films, the spherical colloidal crystals were transformed greatly under pressure, which lead to obvious change in the optical properties of colloidal crystals. Besides their special symmetry and optical properties, these nonspherical colloidal crystals can be used as templates for 2D or 3D structures of special symmetry, such as 2D nano-networks. We anticipate that this fabrication technique for nonspherical colloidal crystals can also be extended to nonspherical porous materials.     

Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions

Three-dimensional (3D) DNA crystals have been envisioned as programmable biomaterial scaffolds for creating ordered arrays of biological and nonbiological molecules. Despite having excellent programmable properties, the linearity of the Watson-Crick B-form duplex imposes limitations on 3D crystal design. Predictable noncanonical base pairing motifs have the potential to serve as junctions to connect linear DNA segments into complex 3D lattices. Here, we designed crystals based on a template structure with parallel-stranded noncanonical base pairs. Depending on pH, the structures we determined contained all but one or two of the designed secondary structure interactions. Surprisingly, a conformational change of the designed Watson-Crick duplex region resulted in crystal packing differences between the predicted and observed structures. However, the designed noncanonical motif was virtually identical to the template when crystals were grown at pH 5.5, highlighting the motif's predictability. At pH 7.0 we observed a structurally similar variation on this motif that contains a previously unobserved C-G?G-C quadruple base pair. We demonstrate that these two variants can interconvert in crystallo in response to pH perturbations. This study spotlights several important considerations in DNA crystal design, describes the first 3D DNA lattice composed of A-DNA helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful for designing dynamic crystals or biomaterial assemblies.     

非传统型液晶分子设计与工程研究进展

从液晶基元连接方式、液晶分子拓扑结构以及凝聚态自组织方式等方面扼要介绍和评述了非传统型液晶分子设计与工程研究进展,并重点介绍了可望引起液晶显示技术革命的双轴向列相香蕉形液晶研究的突破性工作,展望了非传统型液晶分子设计和复杂自组织超分子液晶领域今后的发展方向。     

On the use of correction factors for the mathematical modeling of insulator based dielectrophoretic devices

Mathematical modeling is a fundamental component in the development of new microfluidics techniques and devices. Modeling allows for the rapid testing of new system configurations while saving resources. Microscale electrokinetic (EK) techniques have significantly benefited by the advances in modeling programs and software packages. However, EK phenomena are complex to model, as they dynamically affect system characteristics, including the physical properties of the particles and fluid within the system. Insulator‐based dielectrophoresis (iDEP) is an EK technique that has received important attention during the last two decades. In particular, numerous research groups that study iDEP systems employ a combination of modeling and experimentation for developing new iDEP systems. An important fraction of these research groups has adopted the practice of employing “correction factors” to account for EK phenomena that cannot be accurately predicted in their models due to model complexity and limitations in computing resources. The present review article aims to provide the reader with an overview of the most common approaches in the use of correction factors for the modeling of iDEP systems.     

Adsorption-Inhibition of Clathrate Hydrates by Self-Assembled Nanostructures

The mechanism by which safranine O (SFO), an ice growth inhibitor, halts the growth of single crystal tetrahydrofuran (THF) clathrate hydrates was explored using microfluidics coupled with cold stages and fluorescence microscopy. THF hydrates grown in SFO solutions exhibited morphology changes and were shaped as truncated octahedrons or hexagons. Fluorescence microscopy and microfluidics demonstrated that SFO binds to the surface of THF hydrates on specific crystal planes. Cryo-TEM experiments of aqueous solutions containing millimolar concentrations of SFO exhibited the formation of bilayered lamellae with an average thickness of 4.2±0.2 nm covering several μm². Altogether, these results indicate that SFO forms supramolecular lamellae in solution, which might bind to the surface of the hydrate and inhibit further growth. As an ice and hydrate inhibitor, SFO may bind to the surface of these crystals via ordered water molecules near its amine and methyl groups, similar to some antifreeze proteins.     

Structure and Growth of Two-dimensional Ices at the Surfaces Probed by Scanning Probe Microscopy

Scanning probe microscopy(SPM) stands out as one of the most powerful tools for characterizing the solid surface and the adsorbed molecules with ?ngstr?m resolution in real space. In particular, this unique technique provides an unprecedented opportunity for directly probing the low-dimensional ices at surfaces. In this perspective, we first review the recent advances of scanning tunneling microscopy(STM) imaging of various two-dimensional(2 D) ice structures on metal[1-7], insulator[8-12], graphite[13-15] surfaces and under strong confinement[10, 16-19]. We then introduce that noncontact atomic-force microscopy(AFM) with a CO-terminated tip enables atomic imaging of a genuine 2 D ice grown on a hydrophobic Au(111) surface with minimal perturbation[20], paying particular attention to the growth processes at the edges of 2 D ice. In the end, we present an outlook on the future applications of 2 D ice as well as the relation between the 2 D and 3 D ice growth.     

Ice-surface adsorption enhanced colligative effect of antifreeze proteins in ice growth inhibition

This Communication describes a mechanism to explain antifreeze protein's function to inhibit the growth of ice crystals. We propose that the adsorption of antifreeze protein (AFP) molecules on an ice surface induces a dense AFP-water layer, which can significantly decrease the mole fraction of the interfacial water and, thus, lower the temperature for a seed ice crystal to grow in a super-cooled AFP solution. This mechanism can also explain the nearly unchanged melting point for the ice crystal due to the AFP's ice-surface adsorption. A mathematical model combining the Langmuir theory of adsorption and the colligative effect of thermodynamics has been proposed to find the equilibrium constants of the ice-surface adsorptions, and the interfacial concentrations of AFPs through fitting the theoretical curves to the experimental thermal hysteresis data. This model has been demonstrated by using the experimental data of serial size-mutated beetle Tenebrio molitor (Tm) AFPs. It was found that the AFP's ice-surface adsorptions could increase the interfacial AFP's concentrations by 3 to 4 orders compared with those in the bulk AFP solutions.     

Computer simulation of chiral liquid crystal phases VIII. Blue phases of the chiral Gay-Berne fluid

The phase diagram of chiral calamitic liquid crystals was studied in the temperature-chirality parameter plane by means of computer simulation. Bulk systems composed of N = 2048 uniaxial chiral calamitic Gay-Berne molecules, i.e. with interactions described by the Gay-Berne potential and an additive term for the energy of the chiral interaction, were investigated using Monte Carlo (MC) simulations in the canonical ensemble (NVT). A rich polymorphism of chiral liquid crystal phases was observed along an isotherm with increasing chirality parameter describing the strength of the chiral interaction. In addition to the cholesteric phase (N*), for the first time a blue phase I (BP I) could be proven by computer simulation of a many-particle system based on model intermolecular interactions. Additionally, at high values of the chirality parameter, a phase with randomly oriented squirming double twist tubes was found as characteristic for the so-called spaghetti model for blue phase III (BP III). The structures of all phases were characterized by order parameters, a set of scalar and pseudoscalar orientational correlation functions, and especially by visual representations of selected configurations.     

Structure and dynamics of orientational defects in ice I

Orientational defects in hexagonal ice were investigated using molecular dynamics simulations. Energy relaxation during L- and D-defect migration was shown to be associated with improved alignment of water molecules along the local electric fields. Two new forms of defects, an "L+D complex," and a "5+7 defect," were characterized. These forms appear in ice trajectories close to the melting point, and in the course of L- and D-pair recombination process. Defect pair recombination was shown to be a complex process, involving collective H-bond changes in groups of molecules.