Direct-Space Structure Determination of Covalent Organic Frameworks from 3D Electron Diffraction Data

Structure determination of covalent organic frameworks (COFs) with atomic precision is a bottleneck that hinders the development of COF chemistry. Although three-dimensional electron diffraction (3D-ED) data has been used to solve structures of sub-micrometer-sized COFs, successful structure solution is not guaranteed as the data resolution is usually low. We demonstrate that the direct-space strategy for structure solution, implemented using a genetic algorithm (GA), is a successful approach for structure determination of COF-300 from 3D-ED data. Structural models with different geometric constraints were considered in the GA calculations, with successful structure solution achieved from room-temperature 3D-ED data with a resolution as low as ca. 3.78 Å. The generality of this strategy was further verified for different phases of COF-300. This study demonstrates a viable strategy for structure solution of COF materials from 3D-ED data of limited resolution, which may facilitate the discovery of new COF materials in the future.     

How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data

Many crystalline solids cannot be prepared as single crystals of sufficient size and/or quality for structure determination to be carried out using single crystal X-ray diffraction techniques. In such cases, when only polycrystalline powders of a material are available, it is necessary instead to tackle structure determination using powder X-ray diffraction. This article highlights recent developments in the opportunities for determining crystal structures directly from powder diffraction data, focusing on the case of molecular solids and giving particular attention to the most challenging stage of the structure determination process, namely the structure solution stage. In particular, the direct-space strategy for structure solution is highlighted, as this approach has opened up new opportunities for the structure determination of molecular solids. The article gives an overview of the current state-of-the-art in structure determination of molecular solids from powder diffraction data. Relevant fundamental aspects of the techniques in this field are described, and examples are given to highlight the application of these techniques to determine crystal structures of molecular materials.     

Two-dimensional ultraviolet spectroscopy of proteins

Two-dimensional ultraviolet (2DUV) spectroscopy is a novel technology for probing molecular structure. We have developed a generalized quantum mechanics/molecular mechanics (QM/MM) approach to simulate the electronic transitions of protein backbones and aromatic amino acids in aqueous solution. These transitions, which occur in the ultraviolet (UV) region, provide a sensitive probe of molecular structure. The features of 2DUV spectra are accurately characterized and enable us to trace small variations in the structure and dynamics as well as evolution propensity with high accuracy. Various structures and dynamic phenomena are investigated to construct a systematic framework for 2DUV simulation mechanisms, so as to explore further applications of this technique. In this feature article, we summarize the theory and applications of 2DUV spectroscopy we have engaged in recently, present the important roles of 2DUV spectroscopy, and outline directions for future development. We hope this article can offer a platform for more scientists in different research fields to gain a clear overview of 2DUVand further attract more people to explore this promising field.     

Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

Utilization of an evaporative light scattering detector for high-performance size-exclusion chromatography of galacturonic acid oligomers

A high-performance size-exclusion chromatography-evaporative light scattering detector method was used to separate, detect and quantify galacturonic acid (GA) oligomers. In 40 mM acetic acid GA monomer, dimer and trimer could be separated with baseline resolution but polygalacturonic acid (PGA) precipitated and could not be eluted from the column. An NH4OAc, pH 3.7, buffer was developed as the eluent which separated GA oligomers as well as PGA and pectin without precipitation. Linear calibration curves for mono-, di- and tri-GA were produced with this buffer which could be used to estimate masses of tetra-, penta- and hexa-GA, as well as 19mer and 20mer.     

Structural,spectroscopic aspects,and electronic properties of (TiO2)n clusters: A study based on the use of natural algorithms in association with quantum chemical methods

In this article, we propose a stochastic search‐based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO₂)_n clusters with n = 1–12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high‐quality structures for these systems. We have shown that the clusters tend to form three‐dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA‐DFT technique agree well with available theoretical and experimental data of literature. © 2013 Wiley Periodicals, Inc.     

The effect of ionic electrolytes on hydrolytic degradation of biodegradable polymers: Mechanical and thermodynamic properties and molecular modeling

The purpose of this study was to examine the effect of electrolytes on the hydrolytic degradation of synthetic biodegradable polymers and fibers. Both Polyglycolic acid (PGA) and poly(glycolide–lactide) copolymer (PGL) were used for the study. Four different electrolytes were used: NaCl, LiCl, MgCl₂, and ZnCl₂. The electrolyte effect was evaluated in terms of the change in tensile properties, water uptake, and surface morphology of the polymers and fibers. It was found that the NaCl and MgCl₂ solutions significantly retarded the hydrolytic degradation of both PGA and PGL as evidenced in the prolonged retention of tensile breaking strength of these fibers when compared to deionized water control. Increasing the concentration of the electrolyte retarded the hydrolytic degradation rate further. These mechanical property data agreed well with the rate and amount of water uptake of PGA and could be correlated with the chemical potential difference of water between the electrolyte solution and pure water. The effect of electrolyte was further analyzed by theoretical calculation. Semiemperical molecular orbital calculations indicated that hard cations like Mg, Li, and Zn strongly coordinated to the polar sites of the polymer chain segments (? C?O) and severely disrupted their solvation spheres. Such a disruption was reflected in the smaller amount and slower rate of water uptake by PGA, and thus a slower rate of hydrolytic degradation as evident in the retention of tensile breaking strength. © 1993 John Wiley & Sons, Inc.     

TAILORING TISSUE ENGINEERING SCAFFOLDS USING ELECTROSTATIC PROCESSING TECHNIQUES: A STUDY OF POLY(GLYCOLIC ACID) ELECTROSPINNING

Poly(glycolic acid) (PGA) has long been a popular polymer in the tissue engineering field. PGA possesses many favorable properties such as biocompatibility, bioabsorbability, and tensile strength. The traditional fiber formation techniques of melt extrusion and cold-drawing are generally limited to fibers of 10–12 μm in diameter. Electrostatic spinning, or electrospinning, is an attractive approach for the production of much smaller diameter fibers which are of interest as tissue engineering scaffolds. We demonstrate the ability to control the fiber diameter of PGA as a function of solution concentration and fiber orientation, as well as show a correlation between the fiber orientation, elastic modulu, and strain to failure of PGA in a uniaxial model.     

Analysis of the genetic algorithm method of molecular conformation determination

Many important problems in chemistry require knowledge of the 3-D conformation of a molecule. A commonly used computational approach is to search for a variety of low-energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low-energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low-energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade-offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.     

Interfacial and foaming properties of prolylenglycol alginates. Effect of degree of esterification and molecular weight

In the present work we have studied the characteristics of propylene glycol alginates (PGA) adsorption at the air–water interface and the viscoelastic properties of the films in relation to its foaming properties. To evaluate the effect of the degree of PGA esterification and viscosity, different commercial samples were studied—Kelcoloid O (KO), Kelcoloid LVF (KLVF) and Manucol ester (MAN). The temperature (20 °C) and pH (7.0) were maintained constant. For time-dependent surface pressure measurements and surface dilatational properties of adsorbed PGA at the air–water interface an automatic drop tensiometer was used. The foam was generated by whipping and then the foam capacity and stability was determined. The results reveal a significant interfacial activity for PGA due to the hydrophobic character of the propylene glycol groups. The kinetics of adsorption at the air–water interface can be monitored by the diffusion and penetration of PGA at the interface. The adsorbed PGA film showed a high viscoelasticity. The surface dilatational modulus depends on the PGA and its concentration in the aqueous phase. Foam capacity of PGA solutions increased in the order KO > MAN > KLVF, which followed the increase in surface pressure and the decrease in the viscosities of PGA solutions. The stability of PGA foams monitored by the drainage rate and collapse time follows the order MAN > KLVF > KO. The foam stability depends on the combined effect of molecular weight/degree of esterification of PGA, solution viscosity and viscoelasticity of the adsorbed PGA film.     

硬脂酸镍与焦性没食子酸的热致变色反应研究

本文报道了硬脂酸镍(NiSt₂)和焦性没食子酸(Pyrogallic acid,PGA)的热致变色现象,研究了热敏涂层的显色密度随加热温度和时间的变化关系.结果表明,涂层密度随温度的升高和时间的延长而增大.通过溶解度实验和吸收光谱的分析,推测了热致变色的可能产物是NiSt₂和PGA生成的某种分子化合物,该分子化合物随浓度的增加可能形成某种分子聚集体,在可见光区产生新的吸收峰.     

DMF-H_2O缔合体系的~1HNMR研究

DMF水溶液是一种生物分子水溶液的简单生化模型。测量了DMF-H_2O体系不同 温度下全浓度范围的~1H NMR数据，对体系中的缔合情况进行了讨论，基于H_2O, H_2O·DMF, (H_2O)_2和(DMF)_2·H_2O的缔合平衡建立了化学缔合模型，采用最 小二乘法拟合实验数据，联合遗传算法和Levenberg-Marquardt算法对模型参数进 行全局寻优求解得不同温度的缔合平衡常数K，再根据不同温度的K求得缔合平衡的 ΔH和ΔS。为了更好地理解DMF水溶液中分子间的相互作用，还测量了298 K下DMF- CCl_4和DMF-BuOH体系全浓度范围的~1H NMR数据作为比较，结合NMR的基本原理对 各DMF溶液体系~1H NMR的实验现象进行了分析和解释，认为水溶液的特殊结构、氢 键和DMF酰胺基的共轭体系是影响DMF-H_2O体系~1H NMR的主要因素。     

Host-guest complexes of carotenoids with beta-glycyrrhizic acid

The structure, stability, and reactivity of the host-guest complexes between a set of carotenoids and the triterpene glycoside, beta-glycyrrhizic acid (GA), were investigated by different physicochemical techniques: high-performance liquid chromatography, optical absorption, and fluorescence spectroscopy. It has been demonstrated recently that the molecular complexes of GA with a number of drugs are characterized by reduced toxicity and increased therapeutic activity of these drugs. In the present work it was found that carotenoids form 1:2 complexes with GA in aqueous solutions as well as in polar organic solvents, methanol, acetonitrile, and dimethylsulfoxide. We assume that the structure of the complex is a cycliclike dimer of GA encapsulating a carotenoid molecule. The stability constants in all solvents are near 10(4) M(-1). In addition, GA forms inclusion complexes with carotenoid radical cations, which results in their stabilization. Complex formation (a) decreases the rate of electron transfer from carotenoids to electron acceptors (Fe3+ or quinone) and (b) considerably increases the lifetime of the carotenoid-quinone charge-transfer complex and the yield of the major product (a carotenoid-quinone adduct). A thermodynamic study shows that hydrophobic interactions are the main driving force of the carotenoid-GA complex formation. These results are important for understanding both the nature of GA complexes and the influence of GA on the therapeutic activity of some drugs. Furthermore, carotenoid-GA complexes could be used for the design of artificial light-harvesting, photoredox, and catalytic systems.     

De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy

We report the de novo determination of 15N-1H bond orientations and motional order parameters for the protein ubiquitin with high accuracy based solely on NMR residual dipolar coupling measurements made in six distinct alignment media. The resulting bond orientations are in agreement with RDC-refined orientations of either solid or solution state coordinates to within approximately 2 degrees , which is also the estimated precision of the resulting orientations. The squared generalized order parameters, which reflect amplitudes of motion spanning the picosecond to millisecond time scales, exhibit a correlation with picosecond time scale order parameters derived from conventional NMR 15N spin relaxation methods. Provided that RDC measurements can be obtained using many different alignment media, this approach (called direct interpretation of dipolar couplings) may significantly impact the attainable accuracy and the molecular weight range accessible to NMR structure determination in the solution state, as well as provide a route for the study of motions occurring on the nanosecond to microsecond time scales, which have been traditionally difficult to study at atomic resolution.     

Multivalent ion/polyelectrolyte exchange processes in exponentially growing multilayers

We show, in this paper that multivalent ferrocyanide anions can penetrate into exponentially growing (PGA/PAH)n multilayer films whatever the nature of the last deposited layer. These ions are not able to diffuse out of the film when it is brought in contact with a pure buffer solution. However, the contact of this film with a poly(allylamine) (PAH) or a poly(L-glutamic acid) (PGA) solution leads to the release of ferrocyanide ions from the multilayer. It is shown that the release of ferrocyanide anions, when the film is in contact with a PGA solution, is due to the diffusion of the PGA chains into the film so that an exchange between ferrocyanide ions and PGA chains takes place inside the film. On the other hand, PAH chains do not diffuse into PGA/PAH multilayers. When the film is then brought in contact with a PAH solution, the PAH chains from the solution are expected to strongly interact with the ferrocyanide ions and thus induce a diffusion mechanism of the multivalent anions out of the film, the film/solution interface playing the role of a sink for these ions. This work thus shows that interactions between multivalent ions and exponentially growing films are much more complex than expected at first sight and that polyelectrolyte multilayers must be seen as dynamic entities in which diffusion and exchange processes can take place.     

Determination of molecular vibrational state energies using the ab initio semiclassical initial value representation: application to formaldehyde

We have demonstrated the use of ab initio molecular dynamics (AIMD) trajectories to compute the vibrational energy levels of molecular systems in the context of the semiclassical initial value representation (SC-IVR). A relatively low level of electronic structure theory (HF/3-21G) was used in this proof-of-principle study. Formaldehyde was used as a test case for the determination of accurate excited vibrational states. The AIMD-SC-IVR vibrational energies have been compared to those from curvilinear and rectilinear vibrational self-consistent field/vibrational configuration interaction with perturbation selected interactions-second-order perturbation theory (VSCF/VCIPSI-PT2) and correlation-corrected vibrational self-consistent field (cc-VSCF) methods. The survival amplitudes were obtained from selecting different reference wavefunctions using only a single set of molecular dynamics trajectories. We conclude that our approach is a further step in making the SC-IVR method a practical tool for first-principles quantum dynamics simulations.     

青霉素酰化酶在介孔分子筛MCM-41上的固定化研究

通过改变酶固定化时的pH值、温度、时间以及酶用量,研究了固定化条件对MCM-41载体上固定化青霉素酰化酶的酶活及其稳定性的影响,明确了酶活及其稳定性随固定化条件的变化规律,初步分析了青霉素酰化酶在介孔分子筛MCM-41上的固定化过程。     

Reinvestigation on the buildup mechanism of alternate multilayers consisting of poly(L-glutamic acid) and poly(L-, D-, and DL-lysines)

The buildup mechanism of polypeptide multilayers prepared by the layer-by-layer deposition of a polyanion (poly(L-glutamic acid) (PGA)) and polycations (poly(L-lysine) (PLL), poly(D-lysine) (PDL), and copoly(DL-lysine)(PDLL)) was reinvestigated by using in situ ATR-IR spectroscopy. A difference spectral technique applied to analyze the spectra indicated that the deposition of both the PGA and PLL (PDL) layers accompanies the formation of secondary structures consisting mainly of the antiparallel pleated sheet (the beta-sheet) structure, and that the formation of the beta-sheet structure cannot always be explained in terms of polyanion/polycation complex formation or charge compensation between the polyanion and polycations, although it has been considered as a major process in the multilayer buildup process. Instead, the present paper proposes the following mechanism. During the deposition of the polyelectrolyte, a small amount of the beta-sheet structures are produced at the interface as a result of charge compensation between a polyelectrolyte and an oppositely charged polyelectrolyte in the multilayer. The beta-sheets act as nuclei from which further propagation of the structure takes place at the solution/multilayer interfaces. The driving force of the buildup process in the new mechanism is a kinetically favorable insolubilization of each polyelectrolyte in solution at the interfaces.     

细菌聚γ-谷氨酸溶液流变性能的研究

用分散聚合法制备了苯乙烯 甲基丙烯酸甲酯微米级单分散共聚物微球 ,粒径为 5 4 μm .将分散聚合体系与乳液聚合体系进行了比较 ,并对共聚物微球的形貌、粒径分布及共聚情况进行了表征研究